Arichard:Notebook/2014/January
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January, 2014[edit]
01/01/2014[edit]
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:
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:
Brain | Timepoint | Run | Lane | NxtIndx # | # Reads | ' | Timepoint | 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:
Run | Lane | NxtIndx | Reads |
HL162 | 1 | 26 | 579859 |
HL162 | 1 | 28 | 1298887 |
HL162 | 1 | 29 | 811001 |
HL162 | 1 | 30 | 353131 |
From AR-MDA-ILMN-Oct24:
Run | Lane | NEBIndx | Reads |
HL162 | 1 | 3 | 847838 |
HL162 | 1 | 4 | 781967 |
01/06/2014[edit]
With respect to the letters after the sample names:
- A = after filter, before lysis
- B = after lysis and staining, before FACS
- C = after FACS
Sample | Sequencing ID | Total reads | >= 1 alignment | fail to align | suppressed | rmdup | % unmapped | % 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[edit]
New brain sort, NeuN+/-, DAPI nuclear stain
- 102 (AD)
- 2410 (AD)
- 62405 (AD)
- M2233 (Down's)
- 1901 (Ctl)