Some Finished To Do List Items portal 9-3-13
2015-01-13++ Some Finished To Do List Items portal 9-3-13
- try out PQRE and HE with MAST with a database that SMC1fs is present in
- find out exact address of flat in Spain
- look at Fulbright
- look at human nr database on Linux computer
- follow up with reserving room and reserving an additional room with Meredith (03-28-2014d1620)
- -https://mail.google.com/mail/u/0/?ui=2&shva=1#search/meredith/144b70d06bd281cb
- make corrections to stem cell autoimmunity paper
-meeting with Stephen about paper 7-28-13
^Didn't I make these corrections? I think I did.
- make feature request for Endnote, Zotero, and Mendeley
see if several peptides all line up with the exact same part of the transcript/protein sequences of the proteins rather than the distribution of alignments
compare HER2 with 4T1 signature
^maybe I don't want to do this as of 12-10-2013d2015
- write up dissertation
- finish SEREX introduction
- finish safety training
- validate tumor sequences
- sequence more of tumor cDNA library to have a more accurate number for the complexity <- maybe
- write up entropy paper
- -organize entropy information for Lu. QC files missing, program not working with spreadsheet, etc.
- I may want to start an overnight culture from 87 from plate 16 since I am low on this sample
- antibody screen positive chimeric transcript pcr with tumor and normal cDNA
- list of pcrs I want to run
- -rbm and 10339 and slain (slain completed) with all 41 minipreps (if none of the 41 are positive then make a new prep of these samples but also make glycerol stock this time)
- -rbm and 10339 and slain for all 96 of some of the positive 41
- I should move data out of genespring soon
- write up stem cell autoimmunity paper
- smc1fs pcr with "6 (6-10-13)" to get all 4 bands for sequencing
- smc1fs pcr with "87" for sequencing to determine orientation information
- make paper revisions
- contact HVI about paper
- find out how column size fractionation works
- determine numbers to see if it is really necessary to make a new library
- In order to do this, I guess I would need a list of all of the transcripts with frameshifts, and then I would need to determine the length of transcript sequence from the introduced stop codon from the frameshift to the end of the transcript. Then I would need to know whether my sequences are long enough on average to capture most of those frameshifts.
- take a look at GPP NIH-Oxford-Cambridge Program mentioned by Mara (January 15th deadline)
- look at home desaturation issue
^I don't think I care about this anymore 5-20-13
- look at representation of library <- I don't know what I meant here anymore
- transform cells with pGEX-SMC1fs soon <- probably no longer applicable <- yeah I think it is no longer applicable 5-20-13
- read dissertation of Muskan
- write outreach summary
- Anesthetic Gas Safety Refresher Training
Completed 4-10-13
powerpoint
"C:\kurt\storage\CIM Research Folder\DR\2013\4-10-13\Isoflurane Training_2013_Update.pptx"
- make note about how to use Deducer software
action: test new agarose
optimize transcript specific amplification
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13d4b4670179cc87
look at HER2 specific peptides from Tiger
https://mail.google.com/mail/u/0/?ui=2&shva=1#search/her2/13c1254a097dce08
optimize transcript pcr
- do 5 more cycles for transcript specific amplification
- do taxes
- leave feedback for Ryan
- stories with lots of good dialogue
- pair programming
- look at sequenced pcomb3xssv3 sequences
- prepare presentation for data club
- work on data club presentation
- do ds cDNA PCR
- email Kathy RNA results (make note about RNA and tape pics into notebook)
- etbr with penny
- music for calm focused energy before challenge
- check whether I have enough 5' oligo
- order new primers for sequencing pSMART2IF vector
order new polyT primer <- actually not necessary
see received random hexamer tumor library clones 2-7-13
- Disease Research for Pathways Teacher Game
- order poly T primer
- read about reverse situps
- make notebook records
- finish pcomb in-fusion
- look at video from Pat
- use free massage from Linda
- analyze CTL data
- finish looking at Hojoon's dissertation
- order primers to sequence whole pcomb plasmid
- look over BDE 791 class to see if I already gave public presentation and just need to do public service
- look at sequences of tumor lib DNA
- go through tumor cDNA library sequences again
Some finished to do list items 2012