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Protected: MERFISH practice talk – Hao

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Thursday 03/26/15

9:00 am – ? Getting Drosophila expression data Failed to find assembled FPKM data downloading 0-4hr data sets from modENCODE What’s with the big time window. There must be better these? need a GTF file for cufflinks to parse the … Continue reading

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Wednesday 04/25/15

9:00 am – 6:00 pm Meetings discussion with patent lawyer discussion with MERFISH team Computer troubleshooting User Profile Disks might be problem with user session management: http://www.virtualizationadmin.com/articles-tutorials/vdi-articles/general/working-with-user-profile-disks-on-session-based-desktop-deployments.html disabled User Profile Disks (these were not enabled on CAJAL but were enabled … Continue reading

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Tuesday 03/24/15

9:00 am – 6:00 pm Literature Gomez-Diaz and Corces 3D genome architecture review Experiment Planning Drosophila Patterning screen started new Projects folder TF interactions Downloaded list of 1000 annotated sequence-specific TFs (GO annotation) from FlyBase. This list has substantial number … Continue reading

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Monday 03/23/15

9:00 am – 7:30 pm Finalizing draft of chromatin manuscript revised gene expression panels in figure 1 added additional references to text wrote figure captions Additional references for chromatin literature P Geyer chromatin organization and function (spatial positioning effects) 2011 … Continue reading

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Tuesday 03/17/15

10:00 am – 12:45 am Chromatin Project wrote code FindDataFiles to return a list of all the folders on data drives. These can be passed to StringFind to find Figure 1 finalizing layout added gene expression bar-graphs (doesn’t look that … Continue reading

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Monday 03/16/15

9:00 am – 11:30 pm Chromatin Analysis re-analyzed C02 data (originally taken on STORM1, not the best data, background separation a bit difficult). looking an Kc CNV this genome is a bit of a mess (not sure how much noise … Continue reading

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Friday 03/13/15

9:15 am – 7:00 pm Chromatin Analysis analyzed up through dot 2 (29) of new D08 data (through dot 64). Looks great. analyzing fractal dimension parameters — computing for all composite Flists (this is very slow so hopefully I’m computing … Continue reading

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Thursday 03/12/15

10:15 am – 10:25 pm Meeting with Guy Nir discuss TAD organization discuss STORM buffers (see lab protocols) discussed STORM analysis – see ZhuangLab Github and tutorials discussed converting Nikon format to matlab format. Jeff says Nikon has a dax … Continue reading

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Wed 3/11/15

9:00 am – 12:15 am Little things # move cells to LN2 storage Fixed MORGAN Remote Desktop (see post with today’s date) Project 2 unofficial report – reviewers satisfied with manuscript revisions project 2 meeting minor text adjustments to project … Continue reading

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