Thursday 05/21/15

11:00 am – 12:00 am

(9am-11am lab volleyball practice)

Chromatin paper

  • discuss revisions with Xiaowei
  • working on critical revisions prior to sending to collaborators
  • sent draft to CW and LM and team

MERFISH

  • update planning meeting with XZ
  • discussion with team
    • should have a new go at addressing isoform variation.
Posted in Summaries | Comments Off on Thursday 05/21/15

Wednesday 05/20/15

9:00 am – 9:50 pm

MERFISH

Playing with deconvolution of Laplacian processing

  • see notes
  • summary: very promising in speed, accuracy, simplicity, and aesthetics.
  • ran new pipeline on 141004 data (saved in folder 150520)
  • rerunning with more stringent selection against background (in folder 150520b). 50 cells ~1 hour run time (largely in saving data).
  • starting pipeline5 script — combine read & warp dax files with rest of analysis. Convert into functions.

For presentation

  • Register for EMBO meeting on nuclear structure and submit abstract
  • highlight differences in structure in summary
    • “compact and diffuse domains, branched and linear domains, domains that are highly entangled with one-another and domains which are strictly segregated”
  • highlight implications
    • short range contacts in Active regions in cultured cells
    • long range interactions in Polycomb domains
    • hox genes more tightly packed than other genes because of colinearity. (better repressed)?
Posted in Summaries | Comments Off on Wednesday 05/20/15

Protected: MERFISH image processing 05/20/15

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Nuclear Structure and Dynamics 2015 Abstract

Nuclear Structure and Dynamics
http://events.embo.org/15-nucleus/

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 development and cell fate selection. Unfortunately, current methods provide little information about the 3D organization of the genome at the length scale of genes (kilobases) and regulatory domains (hundreds of kilobases) in single cells. I will present a new super-resolution imaging approach to study the structural organization of the genome at the kilobase to megabase scale in individual cells at 20 nm resolution. These domains largely occupy diffraction limited volumes and thus their structures cannot be resolved with conventional imaging approaches. From thousands of images of epigenetic domains across the Drosophila genome, we have discovered, within a single cell type, a substantial diversity of structural patterns: compact and diffuse domains, branched and linear domains, domains that are highly entangled with one-another and domains which are strictly segregated. These different structural features are closely correlated to certain differences in the epigenetic state of the chromatin. I will highlight the organization of Polycomb bound domains, which exhibit a surprising, entangled structure and length-dependent compaction. Computational models suggest this organization could contribute to the repressive nature of the domains. Preliminary comparisons between developing tissues suggests differential regulation of chromatin structure is associated with developmental fate selection. Together, our observations reveal rich structural diversity in chromatin packaging, suggest some potential regulatory factors, and highlight the importance of understanding structural organization for the study of gene regulation.

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Protected: Tuesday 05/19/15

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Monday 05/18/15

9:45 am

Chromatin Paper

  • writing first draft of letter to editor
  • working on probe table
  • still need to make primer table.

MERFISH

  • working on revised analysis pipeline

Personal stuff

  • looking at apartments
Posted in Summaries | Comments Off on Monday 05/18/15

Sunday 05/17/15

11:00 am – 1:00 am

Chromatin manuscript

  • computed p-values for overlap figures. Added values to fig caption
    • maybe should go into main text when I get it back from Jeff
  • p-values for overlap fraction for reference
    • Repressed-Active interact less than Silent-Active, p < 1e-14.
    • repressed intradomain interact more than active, p < 1e-26.
    • repressed intradomain interactions more than silent, p < 1e-22.
    • silent intradomain interact more than active, p < 1e-2.
    • silent active interact less than silent-silent, p < 1e-10.
  • p-values for entanglement score for reference
    • Repressed-Active interact less than Silent-Active, p < 1e-4 (~1e-5)
    • repressed intradomain interact more than active, p < 1e-12.
    • repressed intradomain interactions more than silent, p < 1e-9.
    • silent intradomain interact more than active, p = .1 (Not signficant)
    • silent active interact less than silent-silent, p < 1e-4
  • updated linker colors in Extended Data Fig 6
  • computing p-values for for extended data fig 8
Posted in Summaries | Comments Off on Sunday 05/17/15

Friday 05/15/15

9:30 am – 11:55 pm

New Data analysis tools

  • generalized Hi-C plotter with Bogdan
  • now does triangles too
  • uploaded new HiC data. Looks much smoother, replicates with different enzymes look very similar.

HiC_normalization

newDataHigherRes

Chromatin paper

  • working on manuscript revisions
  • discussed plans and progress with LM and team (6pm-8:30pm)

To do still

  • comment on cell cycle and pairing in intro section (may need additional supplemental discussion)
  • add p-values to all comparisons in Fig 2, 3, and Extended Data Fig 8 (and 6 and 7), with N cells per comparison.
    • XZ recommends combining samples of same type for the fig 2/3/6/7 comparisons.
  • check entanglement scores (rerun?)
  • fix connectors
  • combined fasta file
Posted in Summaries | Comments Off on Friday 05/15/15

Thursday 05/14/15

9:00 am – 8:30 pm

morning 9 – 10:45am

  • chat with HC
  • email Geoff, congrats and follow up
  • email DB about potential collaboration
  • create 1 page pdf of recent publication info for K99 update

Chromatin paper methods revision

  • working on description of domain selection, 10:45 am – ?

AllDomainsIn_SuppTable1

EnrichmentAtflanksOfDomains

FactorEnrichment

NewDomainScreening

Posted in Summaries | Comments Off on Thursday 05/14/15

Wednesday 05/13/15

9:00 am – 10:15 pm

Geoff’s Defense (9:30 am – 11:00 am)

  • see post
  • short follow-up discussion with BB and GN

To Do

  • Travel reimbursements
  • write to XZ about LM travel schedule (done)

Chromatin Paper

  • Built new composite data structure (allData.matb) to avoid mixed data sets and crazy indexing.
    • some manual field alignment: print elements to Excel, ID missing fields, annotate back in by hand.
    • built new domainData2 structure which has the library number and positions (just positions was getting very confusing)
  • Completed assembly of Supplemental Figure on Intact Domain Histograms

Extended data Figure revisions (3pm – 5pm)

  • renumbering extended data figures in Main text, figures, and figure captions.
  • Writing new extended data figure captions.

New Extended Data Figure 8:

  • wrote generic bootstrapping function to compute confidence intervals.
  • set confidence intervals to 78% for errorbars, So probability two data points with confidence intervals that just overlap are not different ~.22^2 = 0.05.
  • alternatively could do the traditional SEM and the error bars would be smaller still.

Still to do

  • Write cover letter
  • Write description of domain selection
  • color connecting bars in Fig E6
  • print multiple versions of green/magenta/white contrast for Fig 2 and 3
  • combine probe fasta tables and update probe names with new conventions

MERFISH-lunch

  • Jeff will send script on new probe design for human genome
  • Try building a matlab class to handle library design?
Posted in Summaries | Comments Off on Wednesday 05/13/15