Arichard:Notebook/2014/January: Difference between revisions

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>Andrew
(Created page with "==January, 2014== ===01/01/2014=== Of the nine bulk libraries (3 timepoints, 3 brains), only 5 indexes contained reads. This corresponds to the gel image. I asked Alan to tr...")
 
>Andrew
 
(5 intermediate revisions by the same user not shown)
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===01/01/2014===
===01/01/2014===


Of the nine bulk libraries (3 timepoints, 3 brains), only 5 indexes contained reads. This corresponds to the gel image. I asked Alan to try to sequence them just in case we could get a few reads, since I don't need very many.
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}}
{| {{table}}
Line 40: Line 60:
|  
|  
|}
|}
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)

Latest revision as of 17:30, 5 February 2014

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)