Some+finished+to+do+list+items+2012

> > 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? > fix table 2 of paper > attend to robosep e-mail > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13b42e7922bc8194 > get more human RNA? > make sure I am on track for graduation > look at graduation details > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/13ba476b464d1fd3 > look at SMC hits > 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 > look at SEREX publication from Kathy > https://mail.google.com/mail/u/0/?ui=2&shva=1#search/compare+and+contrast/13b4ce19a56fdfcc > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13ab9238a551fa00 > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13b013bf6219ea9e > look at travel stuff (e.g. follow up with graduate college travel grant?) > pJet cloning? (I'm not so sure this is necessary) > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/13a4b70fd01fdab0 > register to vote > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Miscellaneous/13a2eaa092393f2a > https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/139e2b275e293817 > Automatic DNA microarray gridding based on Support Vector Machines > http://www.researchgate.net/publication/224355444_Automatic_DNA_microarray_gridding_based_on_Support_Vector_Machines > Unsupervised SVM-based gridding for DNA microarray images. > http://www.researchgate.net/publication/38057390_Unsupervised_SVM-based_gridding_for_DNA_microarray_images > www.midnightclashtiger.deviantart.com > > talk to Andrey about poly T in-fusion stop codon issue > L:\storage\Documents\Career\Biodesign Institute\Miscellaneous\Paper Proofreading for Others\Shen's Dissertation\Chapter 3 of Shen's thesis\My revisions > check introduction too > Is it okay to have a primer start with many As or Ts? I have a GC clamp at the end. Here are the primers I want to use. > RPTFC: AAAAAAAAAGCGGCCGCCTAGTAGAACCGTAG > RPTFC2: AAAAAAAAAGCGGCCGCAGAACC > > look at clontech 5' end issue > http://www.azim58.wikispaces.net/Entropy+Analysis+of+QC+Samples+7-20-12 > surveymonkey.com/s/TNCCCXY > Look at Shen's changes to SMC1fs paper (I think this is all done) > https://mail.google.com/mail/u/0/?shva=1#inbox/1373c21d52f8d86d >> discuss how many peptides have with motif are in 108 peptide list > > make Kathy's changes to paper > choosing laser power and gain > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/135ac1b7d2f9317e > https://mail.google.com/mail/u/0/?shva=1#inbox/135ac1b7d2f9317e > see Shen's e-mail from 3-27-12 > https://mail.google.com/mail/u/0/?shva=1#inbox/136a6e76e738a61d > Japan conference > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/136db7842e8b1b02 >> look at the microarray mRNA data for my particular cell line: 4T1 > 3-27-12 e-mail from Stephen > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/13656cfe6e26cb3b > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/136418fddd09ccb9 > ARCS dinner (April 27th) > Committee Meeting (Thursday April 26th) > see 3-26-12 e-mail from John Phillips > enrollment accepted from Christine Carlson on May 26th > https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/1369dfe28bcd50af > analyze colony hyb pictures > "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 read cheek bleed protocol 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)
 * When I do flow cytometry again, ask Penny about appropriate voltages and how to centrifuge and resuspend cells
 * take BDGP survey
 * attend to e-mails
 * Things to do before committee meeting
 * redeem chase money
 * do workplace behavior training
 * Plan stem cell experiment
 * attend to smcfs paper
 * electroporation with stellar
 * order DpnI?
 * 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 reduction to single clone/component.
 * look at Mara's midterm paper
 * update ARCS profile
 * store this info somewhere
 * 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 spots, have a membrane for naive, tumor, secondary, and no antibody)
 * revise pcomb primer 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:
 * ask Andrey questions
 * revise CTL protocol
 * note about quickly renaming files
 * paper author info
 * order clontech kit
 * look at raw data of single lysate experiment for increases
 * check Shen's abstract too
 * look at entropy of qc samples
 * do
 * look at purified sera array data
 * switch axis labels in cross-reactivity figure
 * 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
 * respond to Phils e-mail about this
 * https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/13718926742bf690
 * 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
 * find relative abundance of transcripts
 * GEO can help me find the relative abundance of transcripts
 * Note that Danielle did a lot of this already
 * see whether Rose and Maher scholarship is appropriate for me
 * Also address TopCount decision
 * ARCS Tasks 2012-2013
 * After I am caught up with safety courses, then regain access to both 3rd floor parts and Lebaer's lab
 * take fire safety course (12/29/2010 FIRE FIRE SAFETY/PREVENTION 12 months FIRE)
 * 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
 * move Robosep back to room temperature

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.