AllTiddlers:LaCava Research Wiki — Initiated September 2017

AllTiddlers

25th February 2014 at 4:19pm

Current tiddlers:

%Heavy labeling

01 October 20_Optimize N2102EP for Wes/Jess

01/02/2021_MS samples queue sheet (temporary)

01/03/18 - Protein Assay of L1 Heavy and Light Powder

01/03/2020_Experiment x

01/03/2021_ test pagina Susanna

01/03/2021_test page Samira

01/03/2021_test pagina Alex

01/05/18 - Isotope check for L1 I-DIRT

01/09/19 - anti-ORF1 IP_Native Elution with ORF1 dipeptide

01/09/2020_S-Trap Micro Ulra -High Recovery Protocol (Nasty's IP samples, 300/700 mM NaCl and 100 mM MgCl)

01/09/2020_S-Trap Micro Ulra -High Recovery Protocol (Nasty's IPv samples)

01/10/2020_Mass Photometry_Aldolase_Cross-linking (ethanol, urea, guanidine)

01/11/2021_S-Trap Micro Protocol (Berezikov Group, Joscha Muck)

01/12/18 - Orf2 (LD401) PO with post-PO Nuclease treatment

01/12/18 - Orf2 expression in LD401 and MT302

01/14/19 - Endogenous L1 Element Amplification (eLEAP) assay on PA-1 and MT302

01/17/18 - Orf2 (MT302) PO with different amount of anti-FLAG beads

01/19/18 - Orf2 (MT302) PO with different amounts of beads and peptide

01/22/19 - Endogenous L1 Element Amplification (eLEAP) assay on PA-1 and MT302 with heat inactivation

01/23/18 - Orf2 (MT302) PO with different amount of 3xFLAG peptide

01/24/18 - LD401Heavy/LD259Light mix_I-DIRT Screen

01/29/19 - eLEAP assay on PA-1 (50 and 100mg scale) with heat inactivation

01/31/19 - Endogenous L1 Element Amplification (eLEAP) assay on MT302 and 162T / N

01/31/2018_TP53-3xFLAG_anti-TP53 vs anti-FLAG PO

02/01/18 - MT302Heavy/MT289Light_I-DIRT Manual Screen

02/01/2019 - Lamin B polyclonal Purification

02/01/2019 - Lamin B polyclonal Results

02/01/2019 - Lamin B Sepharose Conjugation

02/01/2019 - Polyclonal Purification

02/05/18 - MT302Heavy/MT289Light_I-DIRT 24-well Screen

02/06/2019 - Nup214 polyclonal purification

02/06/2019 – Nup214 Polyclonal Purification

02/06/2019 – Nup214 Sepharose Conjugation

02/06/2019 Nup214 polyclonal Results

02/06/2020_ Mass Photometry experiments (protein test samples)

02/08/2018_Repeat PO TP53-3xFLAG_antiTP53 vs anti-FLAG Wes vs WB

02/09/2021 Exosome-10 IP (in gell digestion of native page bands

02/1/19 Protocol for Optimizing Transcription Factor Release with Probe Sonication

02/1/19 Protocol for Optimizing Transcription Factor Release with the Q800

02/1/19 Q800r Guide

02/10/2020_S-Trap Micro Ulra -High Recovery Protocol (cross-linked Aldolase)

02/11/2021_LCMS sample queue: Berezikov group, Joscha Muck's samples

02/12/18 - Testing S9.6 antibody against RNA/DNA hybrid

02/13/2018_TP53-3xFLAG Test PO on 8% Tris-Glycine gel

02/21/19 - Cross-linking of anti-ORF2 to Protein G beads

02/22/19 - Orf2 (MT302, PA-1) Test PO using anti-ORF2 Protein G beads

02/23/19 Summary of what remains to be acheived

02/27/19 - PA-1 and MT302 purification for MS

02/28/2019 - ORF2 pAB purification

02/28/2019 - ORF2 polyclonal purification

02/28/2019 - ORF2 polyclonal Results

02/28/2019 - ORF2 Sepharose Conjugation

03/03/2021_Anti-HA recovered

03/03/2021_Anti-HA recovery

03/03/2021_antibody recovery

03/05/2019 - Buffer Idea for IP Screening

03/06/19 - L1 expression in new MT302, LD401 and MT289 powder

03/06/2019 - New USP15 Antibody Beads Comparison

03/07/19- Conjugating Dynabeads with Llama anti-GFP antibody

03/08/19 - CBP80 (NCBP1) anti-GFP IP_50mg scale

03/11/2020_Mass Photometry Aldolase crosslinking with BS3 reaction part 2

03/12/2018_24-well Screen Sonication Test on Wes

03/12/2021 Mass Photometry (Human Her2 ErB2 Protein His tag, stress test, Baubek Spanov)

03/13/19 - NCBP3 IP with GA Crosslinking

03/15/19 - L1 expression in MT289, MT302 and LD401 BB’s from Marty

03/18/2018_CDI Protein Standard Test with anti-GST

03/19/19 - Conjugating and testing anti-ORF1 beads

03/20/19- LD561 PO for MS using Gel Plugs or S-Trap

03/26/2019 ORF2p/ORF1p tandem (LD401 heavy)

03/28/2018_16-well Sonication Test on Wes

03/29/2019 ORF2p/ORF1p tandem (LD401 heavy)

04 June 2020_EXOSC10 purification in NaCl 300mM and 700mM

04/03/19 - anti-ORF1 IP with MT302, PA1, HEK and HeLa cell lines

04/03/2019 ORF2p anti-FLAG IP (LD401 heavy (04/24/14), heavy (08/27/12), heavy (05/02/14), light (05/02/14), LD222

04/08/19 - LD288, LD603 and pCEP-Puro anti-FLAG IP

04/08/2019 ORF2p anti-FLAG IP (LD401 heavy (04/24/14), heavy (08/27/12), heavy (05/02/14), light (05/02/14), LD222

04/09/2020_S-Trap Micro Ulra -High Recovery Protocol (Raghu Chivukula's LysoIP samples, RC9-132)

04/10/2019 PVSA Testing for RNA IP - Tumor 162T and Control MT302 - Zymo w/ Phasemaker

04/11/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 700 mM, 150 mg cell powder) folowed by native page analysis and MP

04/11/2021 Mass Photometry (new anti-FLAG beads, NaCl; 700 mM, 150 mg cell powder, G-250)

04/15/19 - MT302 and LD288 PO testing Llama anti-ORF2 antibody

04/15/2019 ORF2p/ORF1p Tandem IP (LD401 heavy powders 8/27/12, 5/2/14

04/16/2019 ORF2p anti-FLAG IP (LD401 heavy (04/24/14), heavy (08/27/12), heavy (05/02/14), light (05/02/14), LD222

04/19/18 - Cross-linking (XL) of anti-ORF2 to Protein G beads

04/20/18 - Orf2 (LD401) Test PO using anti-ORF2 Protein G beads

04/26/18 - Cross-linking (XL) of anti-ORF2 to Protein G beads

04/27/18 - Orf2 (MT302) Test PO using anti-ORF2 and anti-FLAG Protein G beads and anti-FLAG, anti-STAT3 Epoxy beads with or without XL

04/30/18 - Cross-linking (XL) of anti-UPF1, NCBP1 and PABPAC 4 to Protein G beads

04/30/18 - Cross-linking (XL) of anti-UPF1, NCBP1 and PABPC4 to Protein G beads

05/01/18 - Test PO with anti-UPF1, NCBP1 and PABPC4 Protein G beads in HEK293 cells

05/02/18 - Cross-linking of anti-DNA-RNA hybrid antibody (S9.6) to Protein G beads

05/05/2020_Presentation: Methods used in native mass spectrometry

05/06/19 - ORF2/ORF1 Tandem to check LD401 powder

05/06/2019 - Control Rabbit IgG Conjugation to Dynabeads (Epoxy M270)

05/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 1-10 and 15-24)

05/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute)

05/08/2021 anti-FLAG bead conjugation

05/09/18 - Testing S9.6 Antibody using LD401 Native Elution and Fluorscent Oligo

05/09/19 - L1 expression in LD401, MT302 and MT289

05/10/2018_Testing 16-pin sonicator arm

05/11/2020_Nastya's SDS-PAGE protocol for dummies

05/13/19 - LD401, LD561 and pCEP-Puro anti-FLAG IP

05/13/2019 Orf2p/ORF1p Tandem IP (LD401 SILAC powders 4/24/14, 5/2/14)

05/14/18 - Testing S9.6 beads with fluroscent labeled oligos

05/15/18 - Testing S9.6 Protein G beads with Fluorescent Labeled Oligos and RNase treatment

05/16/19 - LD401, LD561 and pCEP-Puro anti-FLAG IP_400mg Scale

05/16/2019 Orf2p/ORF1p Tandem IP (LD401 SILAC powder 4/24/14)

05/21/18 - Anti-ORF1 and anti-ORF2 Western in Human CRC tissues

05/21/18 - Anti-ORF1 and anti-ORF2 Western in Human CRC tissues

05/23/2019 Conjugation of Dynabeads with anti-TP53 antibody

05/28/19 - 162T and 162N anti-ORF1 IP_Sonication_Beads titration_Time course

05/29/19 - Total protein extraction from LD288 and LD603 for CDI antibody testing

05/29/2018_Extract RNA from anti-ORF1 IP

05/29/2019 Orf2p/ORF1p Tandem IP (LD401 SILAC powder 4/24/14) for EM

05/30/18 - Anti-ORF2, S9.6, rIgG, mIgG Protein G beads

05/30/19 - 06/14/19 - Endogenous L1 Element Amplification (eLEAP) assay on PA-1 and MT302 with heat inactivation

05/30/2019 anti-TP53 IP FLpIn T-Rex vs HEK293 WT (ATCC CRL-1573)

05/31/18 - Orf2 (LD401) Tandem PO with S9.6 beads

06/02/2022_Maxquant: Berezikov group, Stijn Mouton's nuclei samples

06/04/19 - Making and testing anti-FLAG and anti-ORF1 beads

06/05/18 - Orf2 (MT302) Tandem IP using anti-FLAG and S9.6 beads

06/06/2019 - New USP15 Antibody Beads Titration by Western and Coomassie

06/07/18 - Orf2 (MT302) Tandem IP using anti-FLAG and S9.6 beads with RNases treatment

06/07/19 - Making and testing anti-FLAG and anti-ORF1 beads

06/07/2017_Quadruplicate anti-TP53 PO for MS in HEK293

06/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 11-14 and 129-142)

06/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 11-14 and 129-142) 1

06/10/2020_ Mass Photometry (Aldolase crosslinking with BS3, reaction)

06/11/19 - LD567 Large Scale IP

06/12/18 - Effect of RNase H treatment on RNA/DNA hybrid

06/13/18 - Effect of RNase treatment on RNA/DNA hybrid and Orf2 elution

06/15/2018_Bead Wash Test - BSA removal

06/17/19 - Testing new Abmart anti-ORF1 by Western

06/18/18 - Orf2 (LD401, MT302) PO testing antibodies

06/18/2019 CDI Antibody concentration and anti-TP53 bead conjugation

06/18/2019 Flow Cytometry sorting of -/-TP53BP1 cell line

06/19/12018 ORF2 (LD401, MT302) PO with anti-FLAG beads

06/19/18 - Anti-ORF2 Protein G beads

06/19/2017_Quadruplicate anti-STAT3 PO for MS in HEK293 and HeLa

06/20/18 - Isotope check: LD401H and LD401H/LD259L

06/21/2018_Extract RNA from anti-ORF1 IP

06/24/2019 ORF2/ORF1 Tandem IP with sucrose cushion for EM LD401

06/25/19 - Prepare IP Elution for MS Using S-Trap Micro Spin Column Digestion Protocol

06/25/2018 Tandem IP for ORF RNPs

06/27/18 - RNA Methylation Quantification (MT302)

06/28/19 - Sample Prep for PROTIFI

06/28/2019 Grid freezing for CryoEM with LINE-1 Tandem IP complexes

06/29/18 - BSA Standard Stock for Gel

06/29/2018 Bio-Beads and Zeba columns

07/01/19 - L1 IP RNA Preparation - RNeasy MinElute

07/01/2019_L1 IP RNA Prep - Qiagen vs Zymo in MT302 and PA-1

07/02/19 - Prepare Whole Cell Samples Using S-Trap Micro Spin Column Digestion Protocol

07/02/2022_m6A-reader 8 samples

07/03/2019 Anti-TP53 IPs from HEK293 Wild Type testing CDI antibodies

07/05/2019 - Test for Best HEPES Concentration for BI-141 Extraction

07/06/2018_Testing Gibco vs. Sigma FBS

07/06/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder, Nastya and Apostolis)

07/06/2021 MP Exosome-10 tests (NaCl 300 mM, 150 mg cell powder, Nastya and Apostolis)

07/07/2018_Extract RNA from Human Tissue in Trizol

07/07/2020_ Mass Photometry_Aldolase_Cross_linking

07/08/19 - Conjugation of anti-ORF1 Dynabeads

07/09/18 - RNA Methylation in MT302 and LD401 Native Eluates

07/09/2018 Zeba columns and markers for BN PAGE

07/09/2018 Zeba columns test in different salt concentrations

07/10/19 - LD401_anti-FLAG and anti-ORF1 beads titration

07/11/18 - RNA Methylation in MT302 and LD401 Total RNA from Native Eluates

07/12/18 - anti-LaORF1 beads conjugation (Epoxy beads)

07/13/18 - LD288 anti-ORF1 PO (Epoxy beads without XL)

07/13/2018 L1 RNPs' EM (ORF2 (LD401) PO with anti-FLAG)

07/13/2018_Extract RNA from Tumor Tissues (optimize tissue RNA prep conditions)

07/16/18 - Cross-linking (XL) of LaORF1 to Protein G or Protein A beads

07/18/18 - ORF2 (LD401) and RRP6 anti-FLAG PO

07/18/19 - Conjugation and testing anti-FLAG beads

07/18/19 ORF2/ORF1 Tandem IP LD401 with BS3 crosslinking titration

07/19/2018 L1 RNPs EM (Tandem IP)

07/23/19 ORF2/ORF1 Tandem IP LD401 with BS3 crosslinking titration on beads

07/24/18 - anti-LaORF1 beads conjugation (Epoxy beads) with incresing amount of nanobody or AmSO4

07/24/19 - Capturing RNP with mouse anti-ORF1 beads from PA-1 PC - With anti-mIgG beads as a control

07/25/18 - LD288 anti-ORF1 PO (Epoxy beads without XL)

07/25/2018 - Tandem IP for ORF RNPs (Zeba columns, Spin-X filters and RNase treatment)

07/26/19 - BSA Standards in Urea and LDS

07/31/18 - RRP6 Purification: Adhesive vs Suspension Cells

07/31/19 - Conjugation of LaORF1-5, LaG94-10 and anti-FLAG Beads

08/01/19 ORF2/ORF1 Tandem IP LD401 with BS3 crosslinking titration in solution

08/01/2018_Extract RNA from Human Tissues (optimize tissue RNA prep conditions)

08/02/18- Making anti-m6A Protein G beads_080218

08/02/2018 - L1 RNPs crosslinking

08/03/18 - Orf2 (MT302) Tandem IP using anti-FLAG and m6A beads with RNases treatment

08/03/2018 - Sucrose and glycerol density gradient separation

08/03/2021 Exosome-10 IP (NaCl; 300 mM and 700 mM) for MP analysis

08/03/2021 Exosome-10 MP analysis (300 mM and 700 mM NaCl IP)

08/04/2021 Exosome-10 IP (NaCl; 300 mM, 200 mg cell powder) for MP analysis

08/04/2021 Mass Photometry (Exosome-10 IP analysis (NaCl; 300 mM)(200 mg scale))

08/05/19 - Anti-ORF1 IP with MT302 to test different elution buffers for S-Trap

08/05/19 - New LaORF1/LaG94-10 batch testing

08/05/19 - Orf2 (MT302) PO testing LaORF1 beads with or without XL

08/05/2019 - USP15 Antiboy Dialysis and Quantification

08/06/2021 Exosome-10 IP (NaCl 300 mM, 150 mg cell powder, Nastya and Apostolis) SDS-PAGE

08/07/19 - Anti-ORF1 IP using PA-1 PC cells with crosslinked LaORF1 beads

08/09/19 - Capturing RNP with lama nanobodies LaORF1 beads from PA-1 PC - With LaG94-10 beads as a control

08/10/2021 Mass Photometry (Human Her2 ErB2 Protein His tag, Baubek Spanov)

08/13/19 ORF2/ORF1 Tandem IP LD401 with BS3 crosslinking titration in solution

08/13/2018_Extract RNA from CRC tissue, anti-ORF1 IP

08/16/2019 Flow Cytometry sorting of -/- OBSL1 cell line

08/17/18 - RRP6 Purification with Native Elution

08/19/19 - 08/22/19 - Endogenous L1 Element Amplification (eLEAP) assay on PA-1 and MT302 with heat inactivation - Testing washes before TurboDNase treatment

08/20/2018_RNA Tumor IP Test with ORF1

08/22/18 - RRP6 purification followed by gradient for EM

08/23/18 - LD288 IP testing anti-FLAG beads

08/26/19 - Making and testing anti-ORF1 beads

08/29/18 - Orf2(MT302) Purification followed by RNAse treatment

08/29/19 ORF2/ORF1 Tandem IP LD401 Native Elutions Tests

09/01/19 - L1 IP RNA Preparation - Zymo MicroPrep Kit

09/03/19 - 162T and 162N IP using PrG or PrA beads

09/04/18 - Orf2(MT302) Purification followed by RNAse treatment

09/05/2019 - USP15 Antiboy Conjugation to Dynabeads

09/06/18 - RRP6 purification and concentration

09/08/2021 Exosome-10 IP (new anti-FLAG beads vs old anti-FLAG beads, NaCl; 300 mM, 150 mg cell powder) for MP/MS/Zipchip analysis

09/08/2021 Exosome-10 IP (new vs old anti-FLAG beads, NaCl; 300 mM, 150 mg cell powder) SDS-PAGE

09/09/19 - RNVC Testing – RNA Prep from MT302 and 162T

09/09/2019 ORF2/ORF1 Tandem IP with BS3 Crosslinking (gel protocol)

09/10/18 - Conjugating Epoxy beads with anti-ORF1 nanobodies and monoclonal antibody with and without XL

09/11/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 700 mM, 150 mg cell powder) for MP, NativePAGE and SDS_PAGE analysis

09/11/2021 Mass Photometry (new anti-FLAG beads, NaCl; 700 mM, 150 mg cell powder, visit Refeyn)

09/12/18 - Orf2 (MT302) PO with anti-ORF1 beads with or without XL

09/12/19 - abcam anti-ORF2 antibody info

09/12/2018_144T and 157T Test IP with ORF1_pretest

09/12/2021 Exosome-10 IP (new anti-FLAG beads, 100 mM MgCl2, 300 mM NaCl/5 mM Chaps, 150 mg cell powder) folowed by native page analysis and MP

09/12/2021 Mass Photometry (Exosome-10 IP, new anti-FLAG beads, 100 mM MgCl2, 300 mM NaCl/5 mM Chaps, 150 mg cell powder)

09/13/17 - ORF2/ORF1 Tandem for RNA-seq

09/14/19 - Testing abcam anti-ORF2 for Western

09/16/19 - Making and testing abcam anti-ORF2 beads

09/18/19 - Making anti-ORF2 (abcam Clone 9-7) beads with increasing AmSO4 concentration

09/18/2019 ORF2/ORF1 Tandem IP for Mass Photometry (+RNasin)

09/19/19 - Testing anti_ORF2 and LaORF2 beads

09/20/17 - Making new anti-FLAG beads and test PO (LD401, 567, 624)

09/20/18 - Orf2 (MT302) PO with ORF1 beads titration

09/21/18 - anti-ORF1 beads survey

09/22/17 - ORF2 (LD567 and LD624) anti-FLAG IP for RNA-seq

09/24/18 - MT302 and PA-1 PC PO with anti-ORF1 beads

09/25/2018_Extract RNA from CRC Tissue, Trizol extraction and parallel anti-ORF1 IP

09/26/19 - Making_Testing anti-ORF2 beads

09/27/18 - LINE1 glutaraldehyde crosslinking

09/28/2018_144T anti-ORF1 Bead Titration Test

09/30/19 - MT302 PO testing anti-ORF2 beads with or without XL

1. Basic concepts summary

1. Conjugation of new anti-ORF1p antibodies and Dynabeads_Dec 2 2019

1. Detection of endogenous ORF2p in N2102Ep using Streptavidin-polyHRP80_Jan 29 2020

1. Suspension culture and MT302 + LD401 transfection of HEK293TLD cells

1. Test experiment with N2102Ep and NTERA2

1. Tester for ribosomal subunit binding of ORF1p_20200316

1. testing reproducability in mass photometer

1. Testing reproducibility of Bioanalyzer data_Dec 10 2019

1. XL-MS on LD401 using S-trap_25 Sept 2020

1.22.20_100s_super_10..png

1.7.20_1_60s_ultra_6.png

1.7.20_2_120s_high_12.png

1) Capture L1 RNP from DC and PC labelled cells from Spain

10-24-19 – DC matrigel vs PC batch 2 comparison for immunoprecipitations with LaORF1 and mouse anti-ORF1 beads + MT302 vs N2102Ep test

10/01/15 - CDI mAbs and MS data

10/01/19 - Checking and recovery of anti-ORF2 (abcam, clone 9) antibody

10/02/2019 ORF2/ORF1 Tandem IP for Electron Microscopy (EM)

10/02/2021_PhD project description Shaoshuai

10/02/2022_Maxquant: m6a-reader-in-arabidopsis, Dawid Bielewics

10/03/18 - RRP6 purification for EM_Effect of detergent concentration of elution

10/03/2021 Mass Photometry (Exosome-10 IP analysis (NaCl; 300 mM and 700 mM from 19/02/2021)) medium camera settings

10/03/2021 Mass Photometry (Exosome-10 IP analysis (NaCl; 300 mM and 700 mM)) IP buffer contamination

10/05/17 - Total RNA prep with or without RNasin (LD401)

10/05/2019 - Frozen BI-141 T Cell Line and Thymocytes Cryogenic Grinding

10/06/2019 - 6 Conditions Screen USP15 IP on BI-141

10/07/19 - Conjugation of rabbit IgG Dynabeads

10/08/19 - anti-FLAG and anti-ORF2 beads titration test

10/08/2021_LCMS sample queue: Berezikov group, Stijn Mouton's samples

10/09/18- Anti-ORF1 IP with MT302 and PA-1 PC cells: titration of LaORF1 beads

10/09/2018_144T anti-ORF1 Bead Titration Test (repeat)

10/09/2020_ Mass Photometry_Aldolase_Cross_linking_extra information

10/10/14 - LD401 preps and CDI mAbs

10/12/17 - ORF2/ORF1 Tandem for RNA-seq

10/16/17 - ORF2 (LD567 and LD624) anti-FLAG IP for RNA-seq

10/16/18 - ORF2 (LD561)_Test PO with Benzonase treatment

10/16/2018_Triplicate anti-ORF1 PO in 144T

10/17/18 - Isotope check MT302H, MT289L, 302H/289L mix

10/17/19 - Antibody recovery from antibody mix after beads coupling

10/18/18 - LD561 Test PO with Nucleases (Benzonase, RNase A/T1) treatment

10/22/19 - Making and testing anti-ORF1 and mIgG beads

10/23/19 - Making and testing LaORF1 and LaG94 beads

10/24/18 - ORF2 (LD561)_PO for EM_with Nuclease treatment

10/26/17 - LD401Heavy/LD259Light mix_I-DIRT 24-well Screen

10/28/2019 Refeyn Report L1 RNP Mass Photometry

10/29/18 - Conjugating anti-Ring1B

10/29/19 - Making and testing LaORF2 beads nanobodies

10/3 Eriba bead and Pierce bead comparation

10/30/18 - ORF2 (LD561) test PO with different buffer conditons

10/30/19 - Capturing RNP with mORF1 beads from PA-1 DC - With mIgG beads as a control

10/31/17 - STAT3-3xFLAG Large Scale Purification_300mM NaCl

10/31/18 - ORF2 (MT302) test PO with different buffer conditions

11/01/19 - L1 IP RNA Preparation - Zymo MicroPrep Kit

11/02/2020_RRP6 purification for mass spectrometry

11/06/19 - Making and testing LaORF2-12 beads

11/07/17 - STAT3-3xFLAG Large Scale PO_150mM NaCl with control

11/07/18 - LD561 Purification for EM with Nucleases treatment

11/09/17 - NFKB1-3xFLAG test PO

11/12/18 - Isotope check for MT302H, MT289L and 302H/289LMix_SDS

11/12/19 - Making and testing LaORF2-12 and LaORF2-16 beads

11/14/18 - 162T and 162N anti-ORF1 PO and Western of Lysate

11/16/17 - anti-FLAG and anti-NFKB1 Western

11/16/18 - ORF2 (MT302) PO for EM_Urea

11/19/18 - 162T and 164N anti-ORF1 PO for Western (Elution only)

11/20/2019 Novus antibody titrations anti-TP53BP1 and anti-OBSL1

11/27/18 - Pullout with Ring 1B or mouse IgG beads using estrogen induced cells

12 January 22_anti-ORF2 Bead Conjugation and Testing

12 May 2020_Optimize sonication conditions for QSonica Q700

12/04/17 - anti-DACH1 PO and Western

12/04/19 - anti-FLAG, anti-ORF1 and anti-ORF2 beads titration test

12/06/17 - Conjugating Dynabeads with CDI mouse mAbs

12/06/2020_ Mass Photometry experiments (protein test samples)

12/06/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder, Nastya and Apostolis)

12/06/2021 MP Exosome-10 tests (NaCl 300 mM, 150 mg cell powder, Nastya and Apostolis)

12/07/17 - anti-KLF5 and anti-RELA PO and Western in HEK and HeLa

12/08/2019_Cloning experiment MT646

12/08/2019_Cloning experiment MT647

12/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 25-54)

12/11/19 - Reuse anti-ORF1 for beads conjugation

12/19/19 - PA-1, N2102Ep and NTERA2 anti-ORF1 IP

13/03/2020_S-Trap Micro Ulra -High Recovery Protocol

13/04/2021 Bradford Protein Assay (standard 1 mL cuvettes)

13/05/2019 - Bradford Assay to Determine the Clarified Extract Concentration for the USP15 Beads Test

13/05/2019 - Coomassie and Western Blot to Test USP15 Beads by IP

13/05/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder) for MP analysis

13/06/2019 - Ammonium Acetate Conditions Optimization for USP15 IP

13/09/2021_Maxquant: Arthur Flohr Svendsen samples

13/11/2020_S-Trap Micro Protocol (Raghu Chivukula's LysoIP samples, RC10-30, changed protocol)

14/01/2022_LCMS sample queue: Berezikov group, Stijn Mouton's nuclei samples

14/09/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM/500 mM/700 mM, 150 mg cell powder) folowed by native page analysis

15/01/2019_L1 IP RNA Preparation – Zymo MicroPrep kit

15/03/2019_PVSA Testing in 162A and MT302

15/04/19 - Milo Test #2

15/05/2019 - Western Blot and Coomassie for USP15 6 conditions IP (NP-40/Triton-X-100, Sonication and NaCl concentration)

15/05/2020_Presentation: Crosslinking mass spectrometry

15/05/2021 MP Exosome tests (150 mg 300 mM NaCl IP Apostolis)

15/06/2020_S-Trap Micro Ulra -High Recovery Protocol 1

15/06/2021 Exosome-10 IP (NaCl 300 mM, 200 mg cell powder, Nastya and Apostolis)

15/06/2021 MP Exosome-10 tests (NaCl; 300 mM, 150 mg cell powder IP, Nastya and Apostolis)

15/07/2021_S-Trap Micro Ulra High Recovery Protocol rev 5/27/21 (Arthur Flohr Svendsen)

15/10/2020_Presentation MP progress

15/12/2021_microBCA protocol (Stijn Mouton samples)

15/7/20 MgCl2 100 mM 4 samples

16/05/2019 - Bradford Assay to Determine the Clarified Extract Concentration for the USP15 Buffers Test

16/05/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder) Bradford and SDS-PAGE

16/06/2020_S-Trap Micro Ulra -High Recovery Protocol

16/08/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM and 700 mM, 150 mg cell powder) SDS-PAGE

16/08/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM/700 mM, 150 mg cell powder) for SDS-PAGE analysis

16/08/2021_LCMS sample queue: Arthur Flohr Svendsen samples

16/08/2021_LCMS sample queue: Universal Protein Standard (300 mM NaCl IP samples, Apostolis and Nastya cell powder)

16/08/2021_Maxquant: Berezikov group, Stijn Mouton's samples

16/11/2020_Protocol Mass Photometry Experiments

16/11/2021 SDS-PAGE (new anti-FLAG beads, NaCl; 700 mM, 150 mg cell powder, visit Refeyn)

16/11/2021_Maxquant: Berezikov group, Joscha Muck's samples

17 May 21_N2102EP Drug Assay Cell Growth, Drug Dosage and Harvest

17/04/2021_LCMS sample queue: Berezikov group, Joscha Muck's samples

17/04/2021_S-Trap Micro Protocol (Berezikov Group, Joscha Muck)

17/06/2019 - USP15 IP in BI-141 Samples Preparation for MS (Including Silver Stain Control)

17/09/2021 Exosome-10 IP 300 mM new beads (in gell digestion of sds-page bands)

17/09/2021 Exosome-10 IP 300, 500 and 700 mM (in gell digestion of native page bands)

17/12/2020_LCMS sample queue: Hua's N2102EP anti-ORF1 IP with Nuclease treatments

17/8/20 NaCl 300, 700 mM and MgCl2 100mM protocol

18/01/2019_RNA FOR Zbig

18/02/2019 - 21/02/2019_Sabatini Lab Suspension Culture Training

18/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 55 -74)

19/02/2021 Exosome-10 IP (NaCl; 300 mM and 700 mM) for MP analysis

19/02/2021 Exosome-10 MP analysis (NaCl; 300 mM and 700 mM)

19/04/2020_Peptide Selection

19/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 75 -104)

19/12/18 - Milo Test

19/12/2020_LCMS sample queue: Hua's N2102EP L1 screen in 24-well format

197N_268N table.png

197N_268N_pellet_102920.png

2. Detection of endogenous ORF2p in N2102Ep using Streptavidin-polyHRP80_Feb 12 2020

2. Material and Methods

2. Prepping anti-ORF1p IP RNA-seq samples on multiple endogenous cell lines_17 Mar 2020

2. Small-scale transfections of MT302 in suspension HEK293TLD cells_17 Feb 2020

2. Testing of new anti-ORF1p beads_Dec 4 2019

2. Testing Ribonucleoside Vanadyl Complex vs. RNasin_Dec 20 2019

2. XL-MS on LD401 in-gel digestion_11 Nov 2020

2) Capture endogenous L1 from PA-1 cells

20 August 2019_anti-GFP bead conjugation

20 February 2020_Triplicate RRP6 IP

20-04-2020 - Description assay design targeted proteomics for ORF2p and ORF1p

20-04-2020 - Excelsheet with additional information about the peptide selection

20/01/2021_SEPMAG LAB nano validation

20/06/19 - Silver Stain and Western for USP15 IP Test on Grinded Thymocyte Powder

20/06/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder, Nastya and Apostolis)

20/06/2021 MP Exosome tests (150 mg 300 mM NaCl IP Nastya and Apostolis)

20/06/2021 Native PAGE Exosome tests (150 mg 300 mM NaCl IP Nastya and Apostolis)

20/06/21 cell culture for powders

20/08/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM and 700 mM, 150 mg cell powder) NativePage Syphro ruby

20200109_ORF1_std_10s_auto.png

20200109_ORF2_high_10s_auto.png

20200109_ORF2_super_6m.png

20200110_N2102Ep_anti-ORF2 beads.png

20200114_EN49_high_30s.png

20200114_EN49_super_5m.png

20200114_RT11_high_30s.png

20200114_RT11_super_5m.png

20200117_anti_ORF2-11_high_30s.png

20200117_anti_ORF2-11_super_5m.png

20200117_anti_ORF2-5_high_30s.png

20200117_anti_ORF2-5_super_5m.png

20200123_ORF1-2_high_30s.png

20200123_ORF1-2_super_1m.png

20200123_ORF1-2_super_3m.png

20200131_RRP6_sypro_2s.png

20200213_anti-ORF1_anti_ORF2 AbMix.png

20200224_LD401_anti-ORF2.png

20200224_LD401_anti-ORF2.tif

20200227_LD401_anti-FLAG_anti-ORF2_022620.png

20200227_LD401_anti-FLAG_anti-ORF2_022620.tif

20200304_anti-ORF2_SEC_030320.png

20200304_anti-ORF2_SEC_030320.tif

20200610DNA OutputMS Exploris

20200610DNA Samples Wouter and Steven - explanation

20200611_CRC_anti-ORF1_hgih_10s.png

20200617_anti-ORF1_std_10s_auto.png

20200617_anti-ORF2_super_3m.png

20200618_CRC-2_high_10s_auto.png

20200618_MeOHppt_10s_auto.png

20200619_1-8 high_10s_auto.png

20200619_9-16 high_10s_auto.png

20200624_MT302_MeOHppt_high_10s_auto.png

20200625_1-8-2nd_3000_high_1m_auto.png

20200625_1-8-2nd_3000_super_5m_auto.png

20200625_9-16 bottom_super_5m_png.png

20200630_MT302_N2102Ep_NTERA_2s.png

20200701_MeOHppt_3rdTrial_high_10s_auto.png

20200702_LaORF1_LaG94_2s.png

20200710_anti-FALG_anti-ORF1_IP.png

20200710_anti-FALG_anti-ORF1_IP.tif

20200713_anti-FLAG beads.png

20200713_anti-FLAG beads.tif

20200714_N2102Ep_NTERA_MeOHppt_2s.png

20200714_N2102Ep_NTERA_MeOHppt_2s.tif

20200716_1021.Nup98_3xFLAG

20200716_1021.Nup98_3xFLAG.png

20200716_1021.Nup98_PKACA_FLAG_Abmix.tif

20200717_N2102_NTERA_MeOHppt_90percent_2s.png

20200717_N2102_NTERA_MT302_0.5s.png

20200717_N2102_NTERA_MT302_0.5s.tif

20200717_N2102_NTERA_MT302_2s copy.tif

20200724_CDI Protein_2s.png

20200730_anti-ORF1_high_10s_auto.png

20200730_anti-ORF1_high_2m_auto.png

20200731_MT302 lysate.png

20200731_MT302 lysate.tif

20200805_N2102Ep_NTERA_Sypro_2s.png

20200814_3xFLAG_7K_40K.png

20200818_Bead testing Leila/Lars

20200820_RRP6_3xFLAG_3s.png

20200827_3xFLAG_BSA_destain ON.png

20200827_3xFLAG_BSA_rerun with fixing.png

20200828_3xFLAG_BSA_no fixing.png

20200828_3xFLAG_no fixing.png

20200904_anti-FLAG_AbMix.png

20200904_MT302_anti-FLAG_label.png

20200910_anti-FLAG beads_XL.png

20200910_RRP6_1s.png

20200918_RRP6_300-500_0.5s.png

20200922_LD401Tandem_2s.png

20200922_LD401Tandem_2s.tif

20200924_N2102Ep anti-ORF1.png

20200924_RRP6_RNaseA-T1-1s.png

20201001_LD401Tandem_2s.png

20201001_N2102_NTERA_PA1_2s.png

20201009_anti-ORF1_anti-ORF2_high_20s_auto.png

20201009_anti-ORF2_super_5m_label.png

20201013_anti-ORF1 IP_high_10s_auto.png

20201013_N2102Ep_anti-ORF1_IP_Super_1m_auto.png

20201013_N2102Ep_anti-ORF2_high_1m_auto_2nd.png

20201013_N2102Ep_anti-ORF2_super_2m_2nd.png

20201013_N2102Ep_anti-ORF2_top_super_5m_1st.png

20201021_2102Ep_NTERA_anti-ORF2_super_3m_label.png

20201021_2102Ep_NTERA_ORF1_ORF2_std_30s_auto.png

20201021_anti-ORF2_9-7_Super_4m_label.png

20201030_197N_268N.png

20201106_RRP6_BSA_2s.png

20201112_401Tandem_E_Zeba40k.png

20201112_401Tandem_RNase_OnBeads-2s.png

20201112_anti-ORF1_high_10s_auto.png

20201112_anti-ORF2_high_5m_auto.png

20201113_401Tandem_NativeElution_2s.png

20201119_N2102Ep_anti-ORF1_Nulceases_2s.png

20201120_ORF2_ORF1_NativeElution_1s.png

20201120_ORF2_ORF1_NativeElution_3s.png

20201124_N2102_anti-ORF1_Nucleases_Sup_2s.png

20201208_L1 Screen_1-24_2s.png

20201208_L1 Screen_1-24_2s.tif

20201219_E_anti-ORF1_anti-ORF2_high_10s_auto.png

20201219_E_anti-ORF2_super_3m_auto.png

20201219_Input_anti_ORF1_high_30s_25ug.png

20201219_Input_anti_ORF1_high_30s_3ul.png

20201219_Input_anti-OR1_super_5m_3ul_auto.png

20201219_Input_anti-OR1_super_5m_auto_25ug.png

20210108_anti-ORF1_high_10s_no adj.png

20210108_anti-ORF1_std_10s_auto.png

20210129_LD288_anti-ORF1_std_10s_auto.png

20210129_SLE_anti-ORF1_E_LDS.png

20210129_SLE_anti-ORF1_E.png

20210211_LD401 Tandem_2s.png

20210223_E_LDS_2s.png

20210223_std_10s.png

20210223_wash1_membrane.png

20210223_wash2_membrane.png

20210223_wash2_std_10s.png

20210223_wash3_regularECL_high_10s_auto.png

20210223_wash3_regularECL_std_10s_auto.png

20210223_wash3_regularECL_std_10s_auto.tif

20210225_LD401 anti-ORF1_anti-ORF2.png

202103 Cloning CMV Clean Tags EN RT ENRT ORF2p mutants pMT868-870

20210305_N2102Ep L1 Screen_anti-ORF1_1s.png

20210305_N2102Ep L1 screen_mIgG_1s.png

20210309_SLE_std_20s_auto.png

20210310_LD288 anti-ORF1.png

20210310_LD288_anti-ORF1_std_10s_auto.png

20210310_RRP6_gradient.png

20210310_SLE_700_1s.png

20210311_RRP6_F9-10.png

20210323_anti-ORF1_high_10s_auto.png

20210323_S9.6 blot_20m_ultra_overlay.png

20210323_S9.6 blot.png

20210323_S9.6_ultra_2m_auto.png

20210326_LD401Tandem_1s.png

20210331_anti_ORF2_super_10m_auto.png

20210331_MT289_N2102Ep_anti-ORF2_high_60s_auto.png

20210331_MT289_N2102Ep_high_10s_label.tif

20210331_MT289_N2102Ep_high_10s.png

20210402_MT289_N2102Ep_MT302_high_10s_auto.png

20210402_MT289_N2102Ep_MT302_high_60s_auto.png

20210407_anti-ORF1_S9.6_anti-ORF1_high_60s_auto.png

20210407_anti-ORF1_S9.6_high_10s_auto.png

20210407_anti-ORF1_S9.6.png

20210412_MT289_anti-ORF1 beads.png

20210413_RRP6.png

20210416_SLE_0.5ul.png

20210416_SLE_15ul-3.png

20210416_SLE_45ul_Ponceau-2.png

20210416_SLE_45ul.png

20210422_SLE_anti-ORF1_1-500_super_15m_auto.png

20210422_SLE_anti-ORF1_super_5m_auto.png

20210429_N2102Ep.png

20210430_N2102Ep anti_ORF1.png

20210504_LD401_Zn.png

20210505_N2102_NTERA_174T.png

20210506_174T anti-ORF1.png

20210507_CRC_anti-ORF1_high_10s_auto.png

20210512_N2102Ep_174T_anti-ORF1_high_10s_auto.png

20210517_RRP6 dialysis.png

20210519_SLE anti-ORF1_super_5m_auto.png

20210528_anti_ORF1_mIgG beads_Ab mix.png

20210528_Anti-ORF2 beads and ORF2p peptides.png

20210604_anti-ORF1-2_hight_1m_auto.png

20210604_anti-ORF2_MT9_MT5_2sec.png

20210611_LD401 Tandem for EM_1sec.png

20210615_senescent_anti-ORF1_high_30s.png

20210617_646-647_anti-FLAG_anti-ORF1_high_10s_auto.png

20210617_MT646-647_anti-FLAG.png

20210625_197 anti-ORF1_high_30s_auto.png

20210625_197TN anti_ORF1_2s_high resolution.png

20210625_L1 anti-FLAG_anti-ORF1_high_10s_auto.png

20210628 nucleofection, L1 CRISPR

202107 IP screening

202107 IP screening 1

20210701_197N_anti-ORF1_1s_label.png

20210701_197T-mIgG_1s_Label.png

20210707_162N_anti-ORF1_1s_label.png

20210708_162T_anti_ORF1_1s_label.png

20210708_197T_anti-ORF1_1s_label.png

20210710_162T_mIgG-2_1s_label.png

20210720 RT PCR- DNAJB1-PRKACA

20210720_162_197_repeat_1s_label.png

20210817_AbMix_ORF1_GFP_FLAG.png

20210819_anti-ORF1_GFP_FLAG test PO.png

20210820_anti-ORF1_GFP beads extra wash.png

20210820_LD401 anti-ORF2_2s.png

20210820_N2102 anti-ORF1.png

20210820_ORF1_ORF2_high_30s_auto.png

20210827_MT302 anti-FLAG_anti-ORF1.png

20210831_STAT3_thrombin_083021.png

20210902_STAT3_PP7_GST_090121.png

20210903_new anti-ORF1_090221.png

20210909_anti-ORF1 beads.png

20210909_MT302 anti-ORF1-2_high_10s_auto.png

20210914_MT302 anti-FLAG_high_1m_auto.png

20210915 RT, TD PCR- DNAJB1-PRKACA

20210915_MT302 anti-ORF1_091321.png

20210916_MT302_anti-ORF1_091521.png

20210924_646_647_564_ORF1-2_high_10m_label.png

20210924_646_647_564_ORF1-2_high_1m_auto.png

20210924_646,647_564_ORF2_LaminB1_PCNA_15m_label.png

20210924_646,647_564_ORF2_LaminB1_PCNA_1m_auto.png

20210930_anti-FLAG IP 092921.png

20210930_ORF2_LaminB2_ORF1_PCNA_high_20s_auto.png

20210930_ORF2_LaminB2_ORF1_PCNA_high_4m.png

202110 anti-PRKACA beads conjugation

202110 FLC RNA quality

202110 RT-PCR, DNAJB1-PRKACA

20211007_MT646 S9.6_super_2m_auto.png

20211007_MT646_anti-ORF1_ORF2_high_2m_auto.png

20211007_MT646_anti-ORF1_ORF2_high_4m_label.png

20211015_MT646-302 Tandem_high_10s_auto.png

20211022_anti-FLAG_ORF1_high_10s_label.png

20211022_anti-ORF2_high_10s_auto copy.png

202111 FLC WB, DNAJB1/ ORF1p

202111 new anti-PRKACA IP

202112 anti-PRKACA beads conjugation

202112 FLC FLC WB, PRKACA/ DNAJB1

202112 FLC PRKACA IP

202112 FLC PRKACA IP&WB

202112 FLC PRKACA JESS

20220124 stripping PRKACA IP membrane

20220126 Transposase transfection

20220203_anti-orf2_020222.png

20220207_anti-orf2 Ab mix.png

20220207_anti-orf2_IP_646-647-564.png

20220208_anti-ORF1-2_high-30s_auto.png

21 October 20_Dynabeads Final Testing

21/08/2020_S-Trap Micro Ulra -High Recovery Protocol (Marty Taylor_Whitehead Institute_samples 105 -128)

21/10/2021 24 IP screening

22/02/2021_Prepared anti-HA beads

22/03/2021 Exosome-10 IP (NaCl; 700 mM, 150 mg cell powder) for MP analysis

22/05/2019 - Western Blot and Coomassie for USP15 Beads Titration

22/07/2020_S-Trap Micro Ulra -High Recovery Protocol (MgCl2)

22/12/2020_S-Trap Micro Ulra High Recovery Updated Protocol (Nastya's IP buffer screening, part 1)

22/3 Pierce Bead Titration

22/7/20 NaCl 300 mM 3 samples

23 April 21_N2102EP Drug Assay Prep_Pilot Test of Media Volume Increase

23 June 2020_Preliminary Test for ZCCHC8

23 June 2020_RRP6 IP_Preliminary Test for ZCCHC8

23 September 2019_anti-FLAG bead conjugation

23/01/19 - L1 IP RNA preparation, Tumor 162 - Zymo w/ Phasemaker

23/01/2019_162T RNA Preparation - Zymo and Phaselock

23/02/2021_SEPMAG LAB nano validation presentation

23/03/2021 Mass Photometry (Exosome-10 IP analysis (NaCl; 700 mM)(150 mg scale))

23/12/2020_LCMS sample queue: Nasty's IP buffer screening part 1

23/7/20 NaCl 700 mM 3 samples

24 June 2020_Test for ZCCHC8 Hua's and Leila's powder

24 June 21_Organoid Cell Culture Training

24-well Screen Sonication Test on Wes (repeat 05/02/18)

24/01/2022 cell adhesion assay

24/06/19 - USP15 IP on Thymocytes Powder Samples Preparation for MS

24/07/2020_S-Trap Micro Ulra -High Recovery Protocol (NaCl 300/700 mM)

25/03/19 - L1 IP RNA preparation, Tumor 162A + PVSA - Zymo w/ Phasemaker

25/06/2021 Mass Photometry (Native Marker in "PBS with 1 % glycerol" and “NativePage sample buffer 1x”)

250ng loading_072320.png

26 May 21_N2102EP Drug Assay Prep_Dynabeads Testing

26-well gel loading copy.png

26-well gel loading.png

26/06/2020_Presentation:R obust transcriptome-wide discovery of RNrnA-binding protein binding sites with enhanced CLIcliP (ecliP)

26/08/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM/700 mM, 150 mg cell powder) dilution test folowed by native page analysis

27/02/2021_anti-HA bead prepared

27/03/2020_S-Trap Micro Ulra -High Recovery Analysis

27/04/2021_Maxquant: Berezikov group, Joscha Muck's samples

27/05/2021 Powerpoint: Berezikov group, Joscha Muck's samples

27/07/2021_S-Trap Micro Ulra High Recovery Protocol (300 mM NaCl IP samples, UPS2)

27/10/2020_Mass Photometry Aldolase stability test

28 May 21_ROME N2102EP Drug Assay anti-ORF1 IP

28/05/2020_repair visit

28/09/2021_S-Trap Micro Ulra High Recovery Protocol (300, 500 and 700 mM NaCl IP samples, for ZIPCHIP analysis)

29 September 20_New Dynabeads Testing

29/05/2019 - New USP15 Antibody Conjugation to Dynabeads (Epoxy M270)

29/05/2021_LC-MS sample queue: Rome IP buffer screening, part 1

29/05/2021_S-Trap Micro Ulra High Recovery Protocol rev 5/27/21 (Rome IP buffer screening, part 1)

29/07/2020_Protein Mix for S-Trap training purposes

29/07/2021_S-Trap Micro Protocol (Berezikov Group, Stijn Mouton)

29/07/2021_S-Trap Micro Ultra-High Recovery Protocol rev. 05/27/21 (Berezikov Group, Stijn Mouton)

29/12/2020_LCMS sample queue: Nasty's IP buffer screening part 2

29/12/2020_S-Trap Micro Ulra High Recovery Updated Protocol (Nastya's IP buffer screening, part 2)

29/12/2021_S-Trap Micro Ultra-High Recovery Protocol rev. 05/27/21 (Berezikov Group, Stijn Mouton, nuclei)

3. Creating content

3. Detection of endogenous ORF2p in N2102Ep using Streptavidin-polyHRP80_Feb 27 2020

3. Testing of VRC depletion after a-ORF1p IP_Jan 28 2020

3) Tet-ON PA-1 cells

30 August 2021 N2102EP Suspension Culture Trial

30 June 2020_Triplicate test for ZCCHC8

30/05/2019 - USP15 Antibody Conjugation to Protein A Dynabeads

30/05/2021_LC-MS sample queue: Rome IP buffer screening, part 2

30/05/2021_S-Trap Micro Ulra High Recovery Protocol rev 5/27/21 (Rome IP buffer screening, part 2)

30/06/2021 Exosome-10 IP (NaCl; 300 mM, 150 mg cell powder, Nastya and Apostolis)

30/06/2021 Native PAGE Exosome tests (150 mg 300 mM NaCl IP Nastya and Apostolis)

30/10/2018_Duplicate anti-ORF1 PO in 144T

31/03/2021 sigma Anti-3xFLAG bead test

3xFLAG-tagged Transcription Factor Constructs & Cell Lines

4 January 22_Large Scale N2102EP and NTERA IPs for PacBio sequencing

4 June 21_BCA Assay of worm nucleii for Stijn (Berezkhov Lab)

4. LINE-1 in PA-1 - Manuscript progression and notes

4. Prep whole cell lysates for targeted MS assay Karin Wolters_14 Aug 2020

4. Tips & tricks

4) Develop more L1 constructs (to use them in the future Tet-ON PA-1 cell line and HEK293T Flp in Trex cells)

5 June 21_Enhanced Protocol BCA Assay of worm nucleii for Stijn (Berezkhov Lab)

5. Prepping new samples for Karin Wolters_10 Oct 2020

5) Wes LINE-1 antibodies/IPs optimization + Wes quantitative analysis (not updated)

5) Wes LINE-1 antibodies/IPs optimization + Wes quantitative analysis + Combined ORF1/ORF2 Wes

50 kDa band checking. ORF1, IgG HC or contaminant

9/04/2021 ORF1 bead test

AbMix_anti-ORF2_anti-GFP_081921 copy.png

AcquireMPUserManual_v2.3.0

AcquireMPUserManual_v2.4.0

Alex Koper's Journal

Amir Zakirov's Journal

Anastasia Petrenko's Journal

Angelica Ferguson's Journal

another 5-codition IP screening

anti-FLAG AbMix.png

anti-FLAG IP loading.png

Anti-HA ercovery

anti-ORF1_090221.jpg

Anti-SMAD4 Test Run on Wes

Apostolis Mourtz's Journal

Application note Detergents

April 1, 2021 - MT289 and N2102Ep Tandem IP using anti-ORF1, S9.6 Protein G and mIgG Epoxy control beads

April 12, 2021 - Testing RRP6 powder

April 16, 2021 - Check SLE Western samples from Seattle

April 19, 2021 - RNA prep with 3'-N-hydroxyurea-3'- deoxythymidine 5'-monophosphate

April 2021 - Iza WT vs HD

April 2021 - Raghu RC10_69

April 2021 HEK293 RRP6-3xflag Dox induction test

April 2021-HEK293 RRP6-3xflag Dox induction test

April 27, 2021- RNA prep from CRC with new RNase inhibitor

April 29, 2021- N2102Ep anti-ORF1 IP with or without new RNase inhibitor

April 30, 2021- N2102Ep anti-ORF1 IP with new RNase inhibitor and mIgG control

April 5, 2021 - Making and testing S9.6 and anti-ORF1 beads

April 8, 2020 - Making and testing new anti-ORF1 beads

April 8, 2021 - Making and testing anti-ORF1 beads

Arianna Picozzi's Journal

Assess tryptic fragments

August 11-27, 2021- Transfection of HEK293TLD in suspension using PEI Max

August 11, 2020 - Comparing anti-ORF1 monoclonal beads and LaORF1 nanobody beads_summary of experimental results

August 16, 2021 - Making and testing anti-ORF1, anti-GFP and anti-FLAG beads

August 18, 2021 - Testing new anti-ORF2 (clone 9-7)

August 19, 2020 - RRP6 purification for EM

August 2020 - Marty samples mTOR lyso IPs

August 2020 - Removing 3x FLAG peptide from native elution

August 2021 – Hua_ORF1 screen in tumors

August 27, 2021 - Testing new MT302 powder

August 30, 2021 - Testing Thrombin Sepharose Beads and Glutathione Resin

August 5, 2020 - anti-ORF1 IP with EDTA or MgCl2

B02-pRS413-DeepStain_014.jpg

Background info_Lars

Basic Notes (from Docollab)

BCA Assay Result.png

Bead preparation ROME test IP/sonication- L1 buffer

Bead testing_Lars

best lab practice

BGG standard.png

Bradford Assay_121620.png

Bufer conditions_041921.png

Buffer conditions_042721.png

Buffer conditions_120420.png

CDI GST-tagged Positive Control Standards

CDI L1 antibodies

CDI L1 Antibodies

CDI Projects Summary Page

CDI recombinant proteins_072120.png

CDI Transcription Factor Antibodies

Cell Culture Protocols

Cell Culture Room Etiquette

Cell culture_Lars

Cell Extracts.png

Cell lines - media - passage - freezing

Cell transfection

Centering an img

Checking GFP tagged yeast samples under the microscopy (12.07.2019-17.07.2019)

Checking RNA integrity with BioAnalyzer at RU

Citing this Wiki - DOI: 10.47673/MacroMolecule

Column Data Thing

Column Data Thing 1

Column Data Thing 2

Conjugation and testing of new a-ORF1P antibodies_Lars

Conjugation of abmart 4H1 anti-ORF1 Dynabeads

Conjugation of antibody Dynabeads

Coomassie stain protocol

CRC 24-well Sonication.png

CRC tissues.png

CRC_pellets_102820.jpg

Creating SubStories

CRYO - 2020 Dec 11 - LINE-1 ORFp2 from Marty

CRYO - 2020 Nov 12 - RRP6 and LD401

CRYO - 2020 Sep 24 - RRP6 and LD401

CRYO - 2021 Feb 11 - LINE-1 ORFp2 from Marty, LD401

CRYO - 2021 Jun 10 - LINE-1 with NanoBodies and ORF2p

CRYO - 2021 Jun 13 - ORF2p

CRYO - 2021 Mar 12 - RRP6 with gradient

CRYO - 2021 Mar 26 - LD401 Tandem with NanoBodies

Debriefing_Lars

December 15, 2020 - N2102Ep, NTERA and CRC anti-ORF1 and anti-ORF2 IPs with controls

December 2020 - Hua samples different RNAse treatments

December 2020 - ROME screen_Hua

December 2020 - ROME screen_Nastya

December 3, 2020 - N2102EP L1 screen in 24-well format

Dennis Nanninga's Journal

Desalting columns.png

Detection of endogenous ORF2p_Lars

DirectZolMicroprep

DiscoverMPUserManual_v2.3.0

DiscoverMPUserManual_v2.4.0

DMP XL of anti-FLAG beads.png

Dot blot grid.png

Draft of '11/19/18 - 162T and 164N anti-ORF1 PO for Western (Elution only)' by admin

Draft of '26/08/2021 Exosome-10 IP (new anti-FLAG beads, NaCl; 300 mM/700 mM, 150 mg cell powder) dilution test folowed by native page analysis 1' by admin

Draft of 'FLC test IP and WB PRKACA' by admin

Dynamic Tables — dynamically created tables that are filterable, sortable, and in-line editable.webarchive

Dynamic Tables Instructions

E-Cadherin Materials

Elution volume for Wes, comparison between ORF1, ORF2 and Flag IPs from PA-1 and MT302

Endogenous a-ORF1 RNA-seq_Lars

ERIBA Stocks and Reagents

Establishing ORF1 as baseline for N2102EP and HEK293T in Milo

Eukaryote Total RNA Nano_2020-08-05_Hua.pdf

EukaryoteTotalRNANano20200805Hua.pdf

Exosome IPs NaCl + MgCl2

Experiments_Lars

Exploris Methods

extra 5-codition IP screening

Extractman Test PO (repeat) 10/20/2017

Extractman Test PO_100217

Feb. 12, 2020 - Testing anti-ORF1_anti-ORF2 beads and RRP6-3xFLAG powder

Feb. 19, 2020 - SEC of ORF2 mAb (9-7)

Feb. 26, 2020 - Testing anti-ORF2 beads

Feb. 5, 2020 - Prepare whole cells and input samples for MS Using S-Trap Micro Spin Column Digestion Protocol

February 10, 2021 - LD401 Tandem IP for EM_test ORF1 nanobody binding

February 16, 2021 - Nucleic acids characterization in L1 RNPs_Collaboration with John Sedivy

February 17, 2021 - L1 RNP preps to capture human auto-antibodies from serum/plasma_2nd test

February 2, 2022 - Anti-ORF2 IP (MT646, MT647, LD564)

February 2022 FLC Sonication optimisation-WB

February 24, 2021 - Making and testing of mouse and rabbit IgG Dynabeads

February 3, 2022 - Making and testing new anti-ORF2 (9-7 and 5-5) beads

Fig1_SEC_021920.png

Fig2_SEC_021920.png

Fig3_SEC_021920.png

FINAL MISO PCR for TP53

FLC Lentivirus plasmid cloning Sept 2021

FLC test IP and WB PRKACA

Flp-In T-REx 293

gel_suspension_culture_lars_20200130.png

Greg House' Journal

Guidelines for manuscript narrative

Han Ly's Journal

HEK 293 Rrp6-3xflag cell culturing & Harvesting

HEK 293 Rrp6-3xflag culturing

HEK293-L1RP-3xFlag/3xAlfa

Hela S3 FlipIn#11 TREX#1,2,3 Testing

Hela S3 Flp-In TREX cell line

HELA S3-FlpIn cell line growth

help bubble.png

help window.png

Historical content from CDI L1 antibodies from Docollab

How to use this Wiki: An evolving Guide

Hua Jiang's Journal

Hua's ORF1-ORF2 screening

Human Cell culture CRISPR Knock Out KO Documentation

Human Cell Culture Mycoplasma Testing

I-DIRT analysis pipeline development for MaxQuant

I-DIRT ORF2p FLAG

Igor Orlov's Journal

Immuno-staining N2102EP ORF1 (leica DM4000b)

Immunoprecipitation with antibody conjugated Dynabeads from cell powder

Infors HT Multitron – How to use + manuals

Initial Tests for Tagged Protein Affinity Capture (from Docollab)

Internship report

IP from PC and DC with different amounts of beads

IP screening robust test

IP-MS RIP-seq ORF1p ORF2p 4H1 cl.9

IssuesWithNewWikiToBeAddressed

Jan. 22, 2020 - Capturing ORF2p with anti-ORF2 beads from N2102Ep

Jan. 29, 2020 - RRP6 purification

Jan. 7, 2020 - Capturing ORF2 with rabbit anti-ORF2 beads from N2102Ep and MT302

January 2021 - Diana Stafa

January 28, 2021 - L1 RNP preps to capture human auto-antibodies from serum/plasma

January 7, 2021 - Large scale N2102Ep, NTERA anti-ORF1 and anti-ORF2 IPs for PacBio Sequencing

Jean-Frederic Olivier's Journal

Jess experiment to test anti-rrp6 Ab

Jess experiment with HEK 293 RRP6-3xFlag Flp-In TREX

John LaCava's Journal

July 15, 2020 - Test Experiment of AmAc/MeOH precipitation_4th trial

July 2021 - CRC 24-well screen_ 162 and 197

July 2021 - Raghu RC10_73

July 2021 - Raghu RC10_93

July 21, 2020 - AmAc/MeOH precipitation of protein from anti-ORF1 elution in organic phase

July 22, 2020 - CDI recombinant proteins

July 28, 2020 - Anti-ORF1 IP with N2102Ep and NTERA2

July 30, 2020 - Optimizing AmAc concentration for protein precipitation

July 6, 2020 - Anti-ORF1 IP with N2102Ep and NTERA2_070820

July 7, 2020 - Testing anti-FLAG and uncoupled beads from ERIBA

June 10, 2020 - CRC (162_185_197_197_268_284) anti-ORF1 IP

June 14, 2021 - Anti-ORF1 IP with senescent cells

June 16, 2020 - Western Blots of Lars' samples

June 16, 2021 - pMT646 and pMT647 anti-FLAG IP

June 17, 2020- CRC (159_185_174) anti-ORF1 IP

June 18, 2020 - Test Experiment of AmAc/MeOH precipitation

June 2020 - IPs exosome

June 2020 – Wouter Huiting Aggregation project

June 2021 Rome Project Anti-ORF1 Bead Test

June 22, 2020 - Test Experiment of AmAc/MeOH precipitation_2nd trial

June 24, 2021 - Checking L1 expression of 9 L1 constructs

June 24, 2021 - CRC-197 anti-ORF1 IP with controls and beads titration

June 28, 2021 - Testing sonication conditions for 50mg powder

June 29, 2020 - anti-ORF1 IP using anti-LaORF1 beads

June 29, 2020 - Test Experiment of AmAc/MeOH precipitation_3nd trial

June 3, 2021 - Testing new anti-ORF2 beads and ORF2 dipeptides_2nd round

June 30, 2020 - Checking LaORF1 and LaG94 beads before and after DMP XL

June 9, 2020 - Summary of anti-ORF1p RNA extractions by Lars

June 9, 2020 - Update on CRC project

June 9, 2021 - LINE-1 tandem prep with or without LaORF1 for EM

June/2021 bead titration

June/2021 IP for BG1 with/without TMTC KO

L1 constructs.png

L1 interatcomes manuscript 2021/2022

L1 pLD401 Tandem IP for EM.docx

L1 samples_March 2021.png

L1 screen buffer conditions.png

L1-related antibody production

Labeled gel.png

Lars ter Morsche's Journal

LC-MS guidelines

Leila Saba's Journal

Lentivirus plasmid cloning FLC Sept 2021

License and Citing this Wiki

LINE-1 antibodies for Wes

Linking to external resources

Luciano Di Stefano's Journal

Luna-FL automated cell counter

LunaFL cell counter

Making powder for MTR4 and CSL4. (12.08.2019-16.08.2019)

Mar. 2, 2020 - SEC of ORF2 mAb (9-7)

March 2, 2021 - N2102EP L1 screen in 24-well format (4x 6 conditions)

March 2021 - ROME screen_second set

March 22, 2021 - N2102Ep Tandem PO with S9.6 beads

March 24, 2021 - LINE-1 tandem prep_with or without LaORF1 for EM

March 30, 2021 - MT289, N2102Ep Tandem PO with S9.6 beads

March 8, 2021 - L1 RNP preps to capture human auto-antibodies from serum/plasma_3rd test with 700ul serum

March 9, 2021 - EXOSC10 (RRP6) gradient for EM

Maria Benitez' Journal

Markup Reference

Marty Taylor's project

Mass Photometry experiments

MATRIGEL preparation

May 10, 2021 - Effects of ZnCl2 and hUdT on IP specificity and RNA quality

May 13, 2021 - Effect of ZnCl2 and hUdT on CRC RNA quality

May 14, 2021 - RRP6 purification followed by dialysis

May 18, 2021 - SLE Neutrophils anti-ORF1 Western

May 2021 ROME assay N2102ep IPs screen anti-ORF1p- drug 12, 473, DMSO

May 24, 2021 - Anti-ORF1 IP with senescent cells

May 25, 2021 - Conjugation of anti-ORF1, anti-ORF2 and mIgG Dynabeads

May 27, 2021 - Testing new anti-ORF1 and mIgG beads

May 27, 2021 - Testing new anti-ORF2 beads and ORF2 dipeptides

May 3, 2021 - LD401 mIgG IP testing effects of ZnCl2 and new RNase inhibitor on IP specificity

May 4, 2021 - Effects of ZnCl2 on IP specificity using different cell lines and tissue

May 5, 2021 - Effects of ZnCl2 on IP specificity using CRC tissue

May, June 2021 - Marty samples mTOR lyso IPs second set

Meeting 25-06-2020

Mehrnoosh Oghbaie's Journal

Merve Duru and Mustafa Kaya's Journal

Milo single west- N2102EP ~ ORF1

ModifiedShadows

Molecular Mass.png

MP Refeyn Model one

MQ pipeline using MT302 as an example

mqpar used for I-DIRT v1

mqpar used for labeling and mixing v1

MS methods guidelines

MS sample preparation protocol using OMIX C18 tips for gel bands

MS sample preparation protocol using OMIX C18 tips for gel plugs

MS sample preparation protocol using Stage Tips for gel plugs

MS sample preparation using S-Trap Micro Protocol rev 10/25/20

MS sample preparation using S-Trap Micro Ultra-High Recovery protocol

MS sample preparation using S-Trap Micro Ultra-High Recovery protocol rev. 05/27/21

MS sample preparation using S-Trap Micro Ultra-High Recovery protocol rev. 12/22/20

ms samples queue sheet

mycoplasma test - DAPI stain

MySubHistoryList

N2102EP 24-well Hand Screen 11-12-2020

N2102Ep 24-well Screen Sonication.png

N2102Ep Cell Viability Assay

N2102Ep drug/DMSO treatment

N2102Ep_cut.png

New anti_ORF1 and anti-ORF2 beads.png

New anti-ORF1 and anti-ORF2 beads.png

New Tiddler 3 - testing edits, John

NFkB1-3xFLAG Cell Line Test

NgSt - 2020 Dec 10 - LINE-1 ORFp2 from Marty

NgSt - 2020 Nov 11 - LD401 with A/T1 on anti-FLAG beads

NgSt - 2020 Oct 01 - LD401 Tandem - spreading experiment

NgSt - 2020 Sep 09 - RRP6

NgSt - 2020 Sep 16 - LD401 Tandem IP, pRS413 plasmid

NgSt - 2020 Sep 23 - RRP6 with RNase A/T1, LD401 - spreading experiment

NgSt - 2021 Feb 10 - LD401 Tandem

NgSt - 2021 Jun 10 - LINE-1 with NanoBodies

NgSt - 2021 Jun 16 - ORF2p and LINE-1 - Various TESTS

NgSt - 2021 Mar 11 - RRP6 with gradient

NgSt - 2021 Mar 25 - LD401 Tandem with NanoBodies

November 10, 2020 - LD401 Tandem IP for EM with RNase A/T1 treatment on anti-FLAG beads

November 17, 2020 - N2102Ep anti-ORF1 IP with Nuclease treatments

November 19, 2020 - Test ORF1 and ORF2 peptide for native elution after RNase A/T1 treatment

November 2020 - Raghu organs RC10_16_and_25

November 5, 2020 - RRP6 purification with BSA incubation

Oct 2020 HEK 293 RRP6-3xFlag Flp-In TREX cell line DOX test induction

October 12, 2020 - N2102Ep anti-ORF1 and anti-ORF2 IPs

October 14, 2021 - MT646 and MT302 Tandem IP with anti-ORF1 and S9.6 beads

October 20, 2020 - N2102Ep and NTERA anti-ORF2 IP for Western

October 2020 - Hua samples ORF1 using different cell lines direct IPs

October 2020 - Hua samples ORF2

October 2021 – Marty lyso I-DIRT reruns sent by Kelly

October 2021 – Marty lyso I-DIRT reruns sent by Kelly 1

October 2021 FLC test IP and WB PRKACA

October 2021 FLC WB PRKACA

October 2021 FLC WB PRKACA Patient A vs B

October 2021 HEK293-L1RP-3xFlag/3xAlfa

October 2021 HelaS3#11 transfection with pcDNA6/TR (tREX)

October 21, 2021 - MT646 S9.6 Tandem IP with RNase treatment before final elution

October 22, 2020- RNA prep from CRC with and without EDTA

October 28, 2020- RNA prep from CRC with DNase I treatment

October 29, 2020 - Checking extraction conditions for 197N and 268N

October 5, 2020 - Summary of materials for CRC project

October 5, 2021 - Effect of RNase treatment on RNA/DNA hybrid and L1 RNP (MT646)

October 7, 2020- L1 endogenous cell line anti-ORF2 and rIgG IPs

Old data 04/02/14 - Orf2 (MT302) with 3x FLAG PO

Omar Rosas Bringas' Journal

ORF1 IP (DC-H-t (B3), PC-H-t (B1), PC-L-ut(B1), PA-1, MT302) with anti-ORF1 beads (50 ug protein)

ORF1, ORF2 and Flag IPs from PA-1 and MT302

ORF1, ORF2 and Flag IPs from PA-1 and MT302 - To test Wes elution/antibody dilutions

ORF1editedforNTERA2.png

ORF1p LFQ screen CRC E, F ORF1p 4H1

ORF1p LFQ screen drug 12, 473 N2102Ep α-ORF1p 4H1

ORF1p LFQ screen N2102Ep α-ORF1p 4H1

ORF2 IP (DC-H-t (B3), PC-H-t (B1), PC-L-ut (B1)) with anti-FLAG beads (Repetition)

ORF2 IP (DC-H-t (B3), PC-H-t (B1)) with anti-FLAG beads

PA-1 - Human Embryonic Carcinoma (hEC) Cells

PA-1 DC culture for getting BBs

PA-1 differentiation

PA-1 PC culture for getting BBs

PC vs DC - LINE-1 expression / silencing

PhD project proposal_Lars

Plasmid maps, primers, sequencing results

Polycarbonate centrifuge bottles

Preparing plasmids 3XFLAG tagged (15.07.2019-24.07.2019)

Preparing stock solutions for yeast strains(02.09.2019-03.09.2019)

Preparing TEV-3C-3XFLAG plasmid(26.08.2019-29.08.2019)

Preparing yeast strains for making noodle(02.09.2019-04.09.2019)

Prior art on %H labeling > Taylor et al. Cell 2013

Project introduction_Lars

Project Summaries

ProteinSimple Equipment

ProteinSimple Jess

ProteinSimple Milo

ProteinSimple Wes

Qsonica Sonicator

Quadruplicate PO of ATF2 and FOXC2 in HeLa for MS

Quantification of electrophoresis gels

Raghu's project

Raghu's projects

Refeyn One Mass Photometer

ReleaseNote AcquireMP v2.3.1

ReleaseNotes_v2.2.0

ReleaseNotes_v2.3.0

ReleaseNotes_v2.4.0

repairs/maintanance

Repeating experiments ( Getting new plasmids 3XFLAG tagged and new yeast strains for GFP tag)(29.07.2019-07.08.2019)

Repeating WB for CSL4 and MTR 4 and making SDS-Page for 5 GFP tagged yeast strain and RRP6 3XFLAG(19.08.2019-06.09.2019)

Ribosomal subunit binding of ORF1p

RNA extraction after cell powder IP

RNA extraction after cell powder IP with on column DNase treatment

ROME test IP/sonication- L1 buffer

ROME, N2102Ep IP buffers preparation

RRP6_Loading.png

S-Trap Micro Protocol rev 10/25/20

S197 L1 Constructs WC Western.jpg

S9.6 Western_super 10m_ with membrane.png

Sam Milano's Journal

Samira Hozeifi's Journal

Screen Shot 2020-07-07 at 13.43.10.png

Screen Shot 2020-07-07 at 13.43.17.png

Screen Shot 2020-07-07 at 13.49.07.png

Screen Shot 2021-09-30 at 3.15.32 PM.png

SEC_anti-ORF2_Peak.png

Sept 2021 Lentivirus plasmid cloning FLC

Sept2021 Hela S3 FlipIn#11 TREX#1,2,3 Testing

September 10-17, 2020 - RNA extraction and MS sample prep in endogenous cell lines following mock IP with mIgG

September 16, 2020 - LD401 Tandem IP for EM

September 17, 2020 - RRP6 purification with 300mM and 500mM buffer

September 2-9, 2020 - Making and testing anti-FLAG beads with antibody from Marty

September 2, 2021 - Concentrating and buffer exchange of anti-ORF1 (4H1)

September 2020 - Hua samples ORF1 using different cell lines after RNA extraction

September 2020 - Raghu RC9 (test)

September 2021 – Hua Senescent cells

September 22, 2020 - Making and testing anti-ORF1 beads

September 23, 2020 - RRP6 purification with RNase A/T1 treatment for EM_092320

September 23, 2021 - Checking L1 expression of MT646, MT647 and LD564

September 29, 2020 - L1 endogenous cell line anti-ORF1 and mIgG for MS

September 29, 2021 - anti-FLAG IP with MT646, MT647, LD564, MT302 and LD401

September 30, 2020 - LD401 Tandem for EM

September 8-15, 2021 - Conjugation of anti-ORF1 Dynabeads and attempt to reduce IgG leakage

September 9, 2020 - RRP6 purification for EM

September-October 2021 – Wouter aggregation project samples for reviewers

service report (shutter stuck)

Shaoshuai Xie's Journal

Simpler Table Macros

SLE samples.png

sonication_50mg-1.png

sonication_50mg-2.png

Spoting grid.png

Spreadsheet of extracted plasmid DNA by Midi/giga preps (Nastya and Lars)

STAT3-3xFLAG PO: anti-FLAG vs anti-STAT3 beads

Subculture Routines for PA-1, N2102Ep Clon 2A6 and NTERA-2 cl. D1

Summary of sonication conditions.png

Susanna Siemonsma's Journal

T1 - Relative protein quantity per mg of powder

T2 - Antibody validation + testing - ORF1p, ORF2p, T7, FOFX2, 3xFlag in DC-H-t (with spare batch 3)

T3 - Antibody validation + testing (OCT4 and FOFX2 in PA-1)

T4 - Determine the relative expression levels & purification profiles of PC-H-t, PC-L-ut and DC-H-t

Targeted Proteomics

Testing of new CDI Antibodies

TF 3xFLAG Flp-In constructs

Thawing Frozen Cells

Thermo Exploris480 LC-MS system

this is new info

Total Protein Extraction with SDS buffer (DC-H-t (B3), PC-H-t (B1), PC-L-ut (B1))

Total Protein Extraction with SDS buffer (DC-H-t (B3), PC-H-t (B1), PC-L-ut (B1))

TP53 Gibson Assembly

TP53 Test PO in HEK293, HeLa, Colon Tumor

TP53-3xFLAG Test PO using anti-FLAG beads

TP53-3xFLAG_Cell Line Induction and Dox Test

Transformation PCR product (3XFLAG) to yeast (02.08.2019-21.08.2019)

Transformation, inoculation protocol

tutorials/instruction videos

useful info for cell culturing

Validating fluorescent antibody using Westernblot and QuantLAS4000

video1_Acquire_mp_1_install_and_setup

video10_mass_calibration.mp4

video11_exporting_data.mp4

video12_movie_variables.mp4

video13_refining_data.mp4

video14_saving_results.mp4

video2_config_and_devices.mp4

video3_file_and_help_settings.mp4

video4_finding_focus_and_calibration.mp4

video5_auto_focus_and_recording.mp4

video6_discoverer_getting_started.mp4

video7_discoverer_batch_process.mp4

video8_discoverer_DiscoverMP_instructional_video.mp4

video9_histogram_toolbar.mp4

WB for 5 GFP tagged yeast strain and BY4741(12.08.2019-13.08.2019)

Wes Manual for L1 detection

Wes Manual for Quantification

Western blot protocol

Why PA-1 DC with matrigel has half the amount of PA-1 DC without matrigel - Rationale of the pre-check assay

WikiBestPractices

Work presentation

Wouter's project

WT Rrp6 Western blot (protein amount oprimisation)

Xiaodong Feng's Journal

xx/06/2020_S-Trap Micro Ulra -High Recovery Protocol

xx/xx/xxxx_Cell Biology Samples Mass Spectrometry Analysis

Ydwine van der Veen's Journal

ZipChip application

Zipchip Repeatability test