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==January, 2014== ===01/01/2014=== Of the eleven bulk libraries (3 timepoints for 3 brains plus positive and negative control), only 6 indexes contained reads. This corresponds to the gel image. I asked Alan to try to sequence them anyways just in case we could get a few reads, since I don't need very many. The libraries sequenced were as follows: {| {{table}} | align="center" style="background:#f0f0f0;"|'''AR-bulk-25,27-Dec11''' |- | AR-bulk-26-Dec11 |- | AR-bulk-28,30-Dec11 |- | AR-bulk-29-Dec11 |- | AR-bulk-31,36-Dec11 |- | AR-bulk-32-Dec11 |- | AR-bulk-37,38-Dec11 |} Index specific info: {| {{table}} | align="center" style="background:#f0f0f0;"|'''Brain''' | align="center" style="background:#f0f0f0;"|'''Timepoint''' | align="center" style="background:#f0f0f0;"|'''Run''' | align="center" style="background:#f0f0f0;"|'''Lane''' | align="center" style="background:#f0f0f0;"|'''NxtIndx #''' | align="center" style="background:#f0f0f0;"|'''# Reads''' | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''Timepoint''' | align="center" style="background:#f0f0f0;"|'''Description''' |- | 1568+||A||HL162||1||25||8460||||A||Before lysis |- | 1568+||B||HL162||3||26||254995||||B||Before FACS |- | 1568+||C||HL162||1||27||65108||||C||After FACS |- | 1864+||A||HL162||3||28||NA|||||| |- | 1864+||B||HL162||3||29||121356|||||| |- | 1864+||C||HL162||3||30||NA|||||| |- | 61788+||A||HL162||3||31||NA|||||| |- | 61788+||B||HL162||3||32||NA|||||| |- | 61788+||C||HL162||3||36||NA|||||| |- | 5 ng E. coli||Pos ctl||HL162||3||37||2636700|||||| |- | NTC||Neg ctl||HL162||3||38||284868|||||| |- | |} Also in HL162, Alan sequenced the rest of the Alzheimer's libraries and the bulk, MDA amplified, Covaris prepped libraries from October. From AR-Alz-26,28,29,30-Sep30: {| {{table}} | align="center" style="background:#f0f0f0;"|'''Run''' | align="center" style="background:#f0f0f0;"|'''Lane''' | align="center" style="background:#f0f0f0;"|'''NxtIndx''' | align="center" style="background:#f0f0f0;"|'''Reads''' |- | HL162||1||26||579859 |- | HL162||1||28||1298887 |- | HL162||1||29||811001 |- | HL162||1||30||353131 |- | |} From AR-MDA-ILMN-Oct24: {| {{table}} | align="center" style="background:#f0f0f0;"|'''Run''' | align="center" style="background:#f0f0f0;"|'''Lane''' | align="center" style="background:#f0f0f0;"|'''NEBIndx''' | align="center" style="background:#f0f0f0;"|'''Reads''' |- | HL162||1||3||847838 |- | HL162||1||4||781967 |- | |} ===01/06/2014=== With respect to the letters after the sample names: * A = after filter, before lysis * B = after lysis and staining, before FACS * C = after FACS {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Sequencing ID''' | align="center" style="background:#f0f0f0;"|'''Total reads''' | align="center" style="background:#f0f0f0;"|'''>= 1 alignment''' | align="center" style="background:#f0f0f0;"|'''fail to align''' | align="center" style="background:#f0f0f0;"|'''suppressed''' | align="center" style="background:#f0f0f0;"|'''rmdup''' | align="center" style="background:#f0f0f0;"|'''% unmapped''' | align="center" style="background:#f0f0f0;"|'''% PCR dup''' |- | 1568+ A||HL162_lane1_indx25||8460||3566||3523||1371||49||41.643026||1.374088615 |- | 1568+ B||HL162_lane3_indx26||254995||180724||15989||58282||694||6.270319026||0.384010978 |- | 1568+ C||HL162_lane1_indx27||65108||32127||20934||12047||446||32.15273085||1.388240421 |- | 1864+ B||HL162_lane3_indx29||121356||82966||6809||31581||548||5.610765022||0.660511535 |- | 5 ng E. coli||HL162_lane3_indx37||2636700||26054||2600174||10472||15050||98.61470778||57.76464267 |- | NTC||HL162_lane3_indx38||284868||27428||247271||10169||16628||86.8019574||60.62417967 |- | |} ===01/20/2014=== New brain sort, NeuN+/-, DAPI nuclear stain * 102 (AD) * 2410 (AD) * 62405 (AD) * M2233 (Down's) * 1901 (Ctl)
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