Athurva Gore/LabNotes/2011-9-23

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Revision as of 21:48, 23 September 2011 by >Ajgore (→‎TO DO)
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TO DO

  • DONE - Design LC Sciences Probes - sent probes to Dr. Zhang, Dinh, and Noi
  • Free space on Genome-Miner, create Shared Folder for HiSeq
    • Still need to reformat Ext6T, ideally before September 26
  • Package Exome Scripts for Thomson Lab
  • Barcoding Padlock Probe libraries - talk to Dinh and Noi
  • Low-input Bisulfite Conversion
  • Paper with Sergio
  • Low-input Exomes (Athanasia) - analyze data?
  • Papers for Doug - ask Dr. Zhang?
  • Review GR Manuscript - by September 28

LC Sciences Probes

  • Turned out I made a mistake in probe design yesterday
    • Some probes were allowed to have arms longer than 40 bp total
  • Redesigned probes for same targets (YX Genes [HORMAD1, ZG16] and Ecker mutation/memory that overlaps with PGP1)
  • Obtained 2199 probes that captured at least one CpG and had fewer than 3 CpGs in probe arms
  • Removed targets with high numbers of probes required (due to C's in arms and large size)
    • Also removed 9 additional probes to make the number to order exactly 4000
  • Probe Set: File:NM LC Probes Filtered 09232011.txt
    • 1820 probes, with 4000 to order due to degeneracy
    • Captures 14,228 CpG sites