Some finished to do list items 2012
2015-01-13azim58 - Some finished to do list items 2012
- When I do flow cytometry again, ask Penny about appropriate voltages
When I finish doing ELISISPOT/T cell assay testing, return CPV172
pooled peptide to Shen.
Things to do during Christmas break
read the other dissertations (read Hojoon's dissertation first)
make notes about committee meeting
organize and write dissertation
work on mouse tumor cDNA library paper?
attend to robosep e-mail
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13b42e7922
bc8194
get more human RNA?
make sure I am on track for graduation
look at graduation details
- take BDGP survey
- attend to e-mails
- Things to do before committee meeting
make actual presentation
look over summary document
look over breast cancer grant document
look at other tumor library sequences
meet with Kathy
I'm curious exactly which pools the single clones came from
https://mail.google.com/mail/u/0/?ui=2&shva=1#search/compare+and+cont
rast/13b4ce19a56fdfcc
- redeem chase money
- do workplace behavior training
51fa00
- Plan stem cell experiment
- attend to smcfs paper
19ea9e
- electroporation with stellar
- order DpnI?
grant?)
- sequence MN pComb
- analyze scanned slide data
- send Kathy e-mail about ova ctl assay
- take care of drivers license issue
- take a look at the data to see if there is an improvement with
- look at Mara's midterm paper
1fdab0
https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Miscellaneous/13a
2eaa092393f2a
- update ARCS profile
293817
- store this info somewhere
http://www.researchgate.net/publication/224355444_Automatic_DNA_microarra
y_gridding_based_on_Support_Vector_Machines
Unsupervised SVM-based gridding for DNA microarray images.
http://www.researchgate.net/publication/38057390_Unsupervised_SVM-based_g
ridding_for_DNA_microarray_images
- check out Diana's artwork
- discuss iPOS with Maria
- Analysis Shen is interested in
- look at Zbig's Tecan run (see Tumor vs normal on Single Clones 9-12-12
- look at papers from Kathy (see 1-5-12 e-mail)
- analyze 16E3 sequences
- redo dot blot (do naive at 10e6 fold dilution, do replicates of
- revise pcomb primer issue
talk to Andrey about poly T in-fusion stop codon issue
- look at A5 spot
- look at tumor intensity distribution
- Mara and I need to look into stop codon issue in 5' cap region
- make mimotope paper revisions
- make record of peptide bead conjugation
- make supplementary heatmap
- revise Shen's paper:
Proofreading for Others\Shen's Dissertation\Chapter 3 of Shen's
thesis\My revisions
check introduction too
- ask Andrey questions
at the end. Here are the primers I want to use.
RPTFC: AAAAAAAAAGCGGCCGCCTAGTAGAACCGTAG
RPTFC2: AAAAAAAAAGCGGCCGCAGAACC
- revise CTL protocol
- note about quickly renaming files
- paper author info
- order clontech kit
- look at raw data of single lysate experiment for increases
look at clontech 5' end issue
- check Shen's abstract too
- look at entropy of qc samples
- do
- look at purified sera array data
https://mail.google.com/mail/u/0/?shva=1#inbox/1373c21d52f8d86d
o switch axis labels in cross-reactivity figure
discuss how many peptides have with motif are in 108 peptide list
make Kathy's changes to paper
- adjust heatmaps so that they are red to green
- adjust cross-reactivity figure so that it is a 3D graph
- perform bone marrow surgery
- look at nci tissue bank info
- look at current protocols in immunology 9.3
- possibly plan ova immunization
- look at optimal laser powers and gains
- look at fastbleep reply
- read about insert to vector ratios with ligation
- Java code to put tab delimited text into some object
- look at current protocols in immunology 9.3
- look at fastbleep e-mail
- look at correlation of tumor on two library array experiments
- work on SMC1fs paper
- make heatmap figure for Shen with 4 peptides and all clinical samples
- https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/1371892
6742bf690
- make context independent sequence annotator
- think about writing article for fastbleep (just do an e-mail search)
- check how often PQRE occurs in all peptides on array
- Kathy's recent e-mail
Japan conference
https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/136db7842e8b1b02
- find relative abundance of transcripts
look at the microarray mRNA data for my particular cell line: 4T1
o Note that Danielle did a lot of this already
- see whether Rose and Maher scholarship is appropriate for me
https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/13656cfe6e26cb3b
- Also address TopCount decision
- ARCS Tasks 2012-2013
Committee Meeting (Thursday April 26th)
- After I am caught up with safety courses, then regain access to both
- take fire safety course (12/29/2010 FIRE FIRE SAFETY/PREVENTION 12
see 3-26-12 e-mail from John Phillips
- and biosafety and bloodborne pathogen training
- write public outreach summary
- read Xiao's proposal if there is time
- make spreadsheet out of Planning 1-26-12 page
- prepare more pmsf and dnase I
"S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research Drive\2012\colony hyb 4-3-12"
I also have some images from March 24th
finish entering immunofluorescence protocol
organize Bart's confocal images
"S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\Raw Data Often
Originally on Research Drive\2012\4-3-12 confocol images"
mailed letter to ARCS donors
write letter to ARCS donors
enter ELISPOT protocol
analyze ELISPOT data
When 2 P50 Biomek tips come in, make sure these are saved for Zbig
analyze SMC1fs data
look at lab manual of Barbas (see 1-5-12 e-mail)
get T cell and phage book
follow up with Topcount and see David Lent's feb 29th e-mail
determine concentration of glycerol stock
make slide-a-lyzer page
perform ELISPOT on T cells from last mouse in old ova group
analyze SMC1fs arrays
analyze decanting results: Test of Decanting after fluor is added 2-3-12
order electrocompetent cells
order 96 well round bottom plates (
http://azim58.wikispaces.com/96+well+round+bottom+plate)
find out amount of reagent used with t cell enrichment kit
If/When cold room is cleared out
- move Robosep back to room temperature
update protocols learned from Bart
research more info about phage (Dec 1st e-mail from Clontech)
read some of PhD Phage Display Cloning Kit
order SAS
analyze ctl data
analyze array data
Renew Phi Kappa Phi Membership
Check to make sure Sfi site on scFv is compatible with PCANTAB site
34 of 39 on SMART cDNA library kit
Hazardous waste management refresher (Nov 17th e-mail)
Order ELISA plates
edit ARCS application
ask robosep about 4 C
buy more antibodies and dyes
ARCS!
Summary of TED event for JoAnne
monoclonal antibody paper from Stephen (10-30-11)
Deal with Robosep software upgrade (Julia October 21st e-mail)
Find restriction sites outside of SfiI and NotI in PCANTAB
Mark has a a plasmid that can be cut with EcoRI and HindII: pET23a with
gp160
- These sites can't be used to cut my PCANTAB for some reason.