Tag Archives: coding

Tuesday 05/29/12

Posted on May 29, 2012 by admin

1:00 P – 4:00P, 9:00P-12:00A running insight analysis on K4 K27 data  (11:00A) using only single iteration for computation of z-calibration curve. compare structure of K4, K27me3 and K27ac chromatin (?) troubleshooting issue with non-convergence of z-calibration bead data by … Continue reading →

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Monday 05/14/12

Posted on May 14, 2012 by admin

10:00A – 8:30P, 9:30-10:30P Eileen Group meeting invitation to SDB to chair postdoc session and speak in regulatory mechanisms section NuGru presentation: Swr1 structural analysis (inserts H2AZ flanking nucleosome depleted regions), for example to protect promoter. Finished 3D bead warping … Continue reading →

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Saturday 05/12/12

Posted on May 12, 2012 by admin

11:30 A – 5:30P Finish DR acceptance statement / bio etc. Literature review: Shandilya transcription review, evidence for transcription factories: Xu 2008 (minichromosomes), Osborne 2004 (DNA / RNA FISH comparison) working on 3D vector bead alignment code

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Friday 05/11/12

Posted on May 11, 2012 by admin

10:55 A -5:15P photos for DRF freeze and clean out fly cages review 3D bead alignment with Sang-Hee Reviewing parameter files.  My default  max displacement don’t match other parameters – might explain low intensities? reset: max_displacement = 1 (160 nm), … Continue reading →

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Thursday 05/10/12

Posted on May 10, 2012 by admin

10:00A -8:00P working on chromatic correction for beads to apply to molecule lists Finished script to merge multiple bead fields from confocal and compute transforms. working on intro sections of ESF talk, formatted to work on laptop. comments back from … Continue reading →

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Wednesday 05/09/12

Posted on May 9, 2012 by admin

12:30 P – 9:45 (volleyball practice 8:30A-11:30A) Pellet and resuspend all new probes. updated probe & plasmid database with new & resynthesized probes: [spreadsheet 0AjSqkxgziU1YdHlnZmFzOVBsX0JQUjlrQnRUWjVYVGc 600 400 sheet=1] 3x maternal Gal4 flies arrived from Perrimon lab -> start expanding coding molecule … Continue reading →

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Tuesday 05/08/12

Posted on May 8, 2012 by admin

10:00A – 10:50 P Bcd Gal4 x shRNA Pc2 and x Psc shRNA1 both still hatch larvae. Flip collection cages check mail for Perrimon Gal4 3x line – not yet arrived rerunning Pc-GFP controls with Colenso’s parameters (min height 750 … Continue reading →

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Thursday 05/03/12

Posted on May 3, 2012 by admin

8:30 A – 8:45P, 10:00P – 11:30P cryo-sectioning: cut 7 slides — embryos mostly around edge.  Need larger cutting surface for good sections. finish STORM run, shoot beads collect virgin Gal4-Bcd3’UTR in situs day 3 fixed issue in list2tif_color_drift_correct: wasn’t … Continue reading →

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Tuesday 05/01/12

Posted on May 1, 2012 by admin

11:00 A – 6:45P, 8:00P -12:00A flip fly collection cages, 11A Miniprep cultured colonies: 8E, 7E, 2E, AbdB2 and Fab8 (2 colonies each).  Send for sequencing. Rearrange ultratome room, suspend on air-table, clean room. Flip collection cages, 3:15 A Analyzing … Continue reading →

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Saturday 04/28/12

Posted on April 28, 2012 by admin

11:00 A – 11:45 P Confocal imaging of Pc-GFP and Pc Reading up on DNA FISH from Bantignies protocol.  10 min denature probe at 95C.  15 min, denature embryos in prehybe at 80C.  Combine hot. wash 1hr at 37 with … Continue reading →

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