Some Finished To Do List Items

2015-01-13

-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
find out how poly A mRNA purification 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.
look at old SMC1fs presence in library data
-take a look at GPP NIH-Oxford-Cambridge Program mentioned by Mara (January 15th deadline)
^I don't think I care about this anymore 5-20-13
-look at home desaturation issue
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Computer+Stuff/13d26ca624edb7ea
^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- probably no longer applicable 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- yeah I think it is no longer applicable 5-20-13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
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13cf3c145d222165
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
-
get Mara data for random hexamer library
-
event:run DNA gel
action: test new agarose
-

optimize transcript specific amplification
-
look at pcomb sequences
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13d4b4670179cc87
-
tomorrow
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
figure out what went wrong with polyT primer
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
https://mail.google.com/mail/u/0/?ui=2&shva=1#search/slick/13c3cdef8e14f7d4
-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

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