Author Archives: admin

Monday 05/20/15

10:00 am – 5:00 pm Meetings discussion with NL about MERFISH 10 am – 11 am reply to E Furlong about MERFISH BWF prep call foundation about slide submission rehearse presentation timing feedback from Jeff on slides feedback from Bogdan … Continue reading

Posted in Summaries | Comments Off

Sunday 05/19/15

5:00 pm – 12:00 am MERFISH Transcriptome building saving additional FPKM data per cell line, per chosen isoform, rebuilding FASTA file with short gene names. running with maxFPKMperType > 1E-5 & maxFPKMperType < 50E3 and fasta length over 2000 bp … Continue reading

Posted in Summaries | Comments Off

Friday 05/17/15

9:00 am – 5:00 pm 9:00 am – 3:00 pm review and prep slides for group meeting journal club lab meeting (see notes) 10am – 1pm reformatting figures for Ph paper Transcriptome design might have been faster to use cufflinks … Continue reading

Posted in Summaries | Comments Off

Protected: lab meeting: 04/17/15

There is no excerpt because this is a protected post.

Posted in Lab Meeting | Comments Off

Thursday 04/09/15

9:00 am – 8:00 pm Ph project Figure making revising layout of Fig 5 sent to team NF says a bit too tight, need more whitespace. re-arranged panels again MERFISH exploring probe selection criteria compare variable length probes to 20mers … Continue reading

Posted in Summaries | Comments Off

Wednesday, 04/15/15

9:00 am – 10:00 pm MERFISH Code development discuss Jeff’s new approach to Library construction Fix indexing in Assemble Oligo Array probes. complete. see Library11CompileOligoArrayResults_150414.m BLAST combos of primers and new Fast Secondaries completed for 5′ fusions. killed half of … Continue reading

Posted in Summaries | Comments Off

Tuesday 04/14/15

10:00 am – 8:20 pm, 9:20pm – 12:00am MERFISH reply to Quake lab with raw data working on fixing lib12 build found bug in my matlab BLAST — allhits field not being populated if no varargin’s passed. fixed. updating MERFISH … Continue reading

Posted in Summaries | Comments Off

SDB 2015 abstract

Super-resolution Imaging of Chromatin Nanostructure Links Epigenetic State and 3D Genome Packaging Metazoan genomes are packaged at multiple scales, and regulation of this spatial organization may play an important role in the developmental and cell fate selection. Unfortunately, current methods … Continue reading

Posted in Summaries | Comments Off

Monday 04/13/15

9:00 am – 6:20 pm, 8:00 pm- 10:30 pm MERFISH design new libraries discussed design with team (9:30-10:30am) working on library assembly (8:00pm-10:00pm) New Libraries (140 gene). 20mer secondaries 30mer targeting regions 1-16 (shorter than before) 20mer secondaries 30mer targeting … Continue reading

Posted in Summaries | Comments Off

Saturday 04/11/15

Ph Project working on simulations Assume certain amount of open sites. All will be fill with no Ph. Add PhM. The same fraction of PhM will be bound as the fraction of Ph bound, since the kinetics are the same. … Continue reading

Posted in Summaries | Comments Off