In this wiki you could find all projects I've worked on during my internships in Groningen.
July-September 2019
It was mostly about cloning MT646 and MT647 and you could find all info you need here:
https://macromolecule-child.rockefeller.edu/#12%2F08%2F2019_Cloning%20experiment%20MT646 https://macromolecule-child.rockefeller.edu/#12%2F08%2F2019_Cloning%20experiment%20MT647
Seq files and other things please find in box (ask John to give you access)
BOX > CLC_Files > L1 > L1_nucleic_acids
Also I extracted different plasmids using zymo midi prep and invitrogen maxi prep
https://macromolecule-child.rockefeller.edu/#Spreadsheet%20of%20extracted%20plasmid%20DNA%20by%20Midi%2Fgiga%20preps%20(Nastya%20and%20Lars) This table has info about what was in ERIBA ~ Dec 2020. So it's better to check plasmid box sometimes or ask Leila about updates. Mostly I filled 260/280 ratio but it's not completely done.
March-December 2020
Mach 2020 was a first month of my second internship but COVID-19 shifted it till May. In May and June I learned how to do Western Blots, commassie stain gels and IP. We partly start the project with Mass Spectrometry analyse of IP samples.
1. First IP with 300 mM and 700 mM NaCl buffers (in Leila's wiki). Here you could find gels, blots. https://macromolecule-child.rockefeller.edu/#04%20June%202020_EXOSC10%20purification%20in%20NaCl%20300mM%20and%20700mM
These IPs were prepared for MS by Dennis via this protocol (Dennis's wiki)
Then they were analysed by Luciano and presented as "IPs June 2020.pptx" during Lab meeting.
2. Then we moved to samples with MgCl2 buffer to repeat https://doi.org/10.1007/978-1-4939-9822-7_25
(from Leila's wiki) https://macromolecule-child.rockefeller.edu/#23%20June%202020_Preliminary%20Test%20for%20ZCCHC8 - first gel of MgCl2 IP samples.
After that we repeated it and got KERATIN contamination. (from Leila's wiki) https://macromolecule-child.rockefeller.edu/#24%20June%202020_Test%20for%20ZCCHC8%20Hua's%20and%20Leila's%20powder
It was decided to repeat it again before ordering new chemicals. So we prepared fresh buffers from the same chemicals and there is no keratin. https://macromolecule-child.rockefeller.edu/#30%20June%202020_Triplicate%20test%20for%20ZCCHC8
These samples are prepared for MS by Dennis https://macromolecule-child.rockefeller.edu/#22%2F07%2F2020_S-Trap%20Micro%20Ulra%20-High%20Recovery%20Protocol%20(MgCl2)
And then run and analysed by Luciano and Dennis
3. We reordered chemicals, prepared buffers again: https://macromolecule-child.rockefeller.edu/#15%2F7%2F20%20MgCl2%20100%20mM%204%20samples and other reports from 15.7.20, 22.7.20, 23.7.20
There are NaCl, MgCl2 IPs with new buffers (4 replicates, will be used for MS and for anti-ZCCHC8 Ab test ) I still have these NaCl 300/700 mM samples in case someone want to do WB.
4. Last IPs 17/8/20 Triplicate experiment NaCl 300/700, MgCl2 100 mM
Wiki protocol https://macromolecule-child.rockefeller.edu/#17%2F8%2F20%20NaCl%20300%2C%20700%20mM%20and%20MgCl2%20100mM%20protocol