Sample QC: Difference between revisions

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Checking clustering of replicates, expression of biomarkers, mapped tag count, promoter hit rate, RIN score.
Checking clustering of replicates, expression of biomarkers, mapped tag count, promoter hit rate, RIN score.


<br>


⚫
'''Library depth check''' - [[Media:Less_than_500000_Q20tags.xls]]


⚫
Human samples with less than 500,000 Q20 mapped tags = '''88'''<br>
⚫
'''Library depth check''' - [[media:Less_than_500000_Q20tags.xls]]

⚫
Human samples with less than 500,000 Q20 mapped tags = '''88'''<br>


*18 macrophage samples from Hume Lab
*18 macrophage samples from Hume Lab
Line 14: Line 14:
*23 commercial primary cells
*23 commercial primary cells


<br>



Mouse samples with less than 500,000 Q20 mapped tags = '''11'''
Mouse samples with less than 500,000 Q20 mapped tags = '''11'''
Line 21: Line 21:
*3 commercial primary cells
*3 commercial primary cells


<br>


⚫
'''Promoter hit rate check (only for samples in release 12 so far)''' - [[Media:Less_than_50percent_promoter_rate.xls]]


⚫
Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology
⚫
'''Promoter hit rate check (only for samples in release 12 so far)''' - [[media:Less_than_50percent_promoter_rate.xls]]


⚫
<br> '''Sample labelling check (by clustering and marker gene checks) ''' <br> Samples were clustered by Kawaji-san
⚫
Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology


⚫
*[[Media:UPDATE_013_human_refseq.pdf]]

⚫
*[[Media:UPDATE_013_mouse_refseq.pdf]]
⚫
'''Sample labelling check (by clustering and marker gene checks) ''' <br>
Samples were clustered by Kawaji-san
⚫
* [[media:UPDATE_013_human_refseq.pdf]]
⚫
* [[media:UPDATE_013_mouse_refseq.pdf]]


Al manually checked these clusters and marker genes.
Al manually checked these clusters and marker genes.
⚫
*1159 human samples look ok so far.
⚫
*104 human samples look questionable (in process of further checks).
⚫
*[[media:Checked_labelling_clustering_ok_human_Nov24.xls]]
Contains lists of putative biomarkers for some of the primary cells and tissue samples.<br>
Eg. [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr8:37998121..38010695 STAR] is a marker of the adrenal gland.<br>
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr20:21683715..21699200 PAX1] is a marker of Anulus Pulposus Cells<br>
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr10:99583300..99832041 CRTAC1] is a marker of re-differentiated chondrocytes<br>
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr14:77934618..77971327 ISM2] is a marker of chorionic membrane cells<br>


⚫
*1159 human samples look ok so far.
⚫
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr5:138835830..138843617 ECSCR] and [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr16:66390983..66448229 CDH5] are global markers of endothelial cells<br>
⚫
*104 human samples look questionable (in process of further checks).
⚫
*[[Media:Checked_labelling_clustering_ok_human_Nov24.xls]]

Contains lists of putative biomarkers for some of the primary cells and tissue samples.<br> Eg. [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr8:37998121..38010695 STAR] is a marker of the adrenal gland.<br> [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr20:21683715..21699200 PAX1] is a marker of Anulus Pulposus Cells<br> [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr10:99583300..99832041 CRTAC1] is a marker of re-differentiated chondrocytes<br> [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr14:77934618..77971327 ISM2] is a marker of chorionic membrane cells<br>

⚫
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr5:138835830..138843617 ECSCR] and [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr16:66390983..66448229 CDH5] are global markers of endothelial cells<br>

<br>

<br>

'''SAMPLES for FREEZE CANDIDATE 1''' Here are the candidates for the phase 1 datafreeze. All samples listed here will be used for tag cluster generation but only a subset flaged 'INCLUDE' will be used in main paper figures.

<br>

*[[Media:Human_Freeze1_samples.xls]]
*988 libraries are included for generating DPI clusters
*889 of these pass further QC measures of Q20 mapped depth &gt;500,000, RNA integrity and reproducibility, and will be used for motif finding and gene expression figures.

<br>

*[[Media:Mouse_Freeze1_samples.xls]]
*402 libraries are included for generating DPI clusters
*397 of these&nbsp;pass further QC measures of Q20 mapped depth &gt;500,000, RNA integrity and reproducibility, and will be used for motif finding and gene expression figures.

<br>

*[[Media:Variome_Freeze1_samples.xls]]



'''Matched samples for Human and mouse comparisons'''

*[[Media:Human_Mouse_counterparts.xls]]

<br>

Latest revision as of 17:51, 11 January 2012

Checking clustering of replicates, expression of biomarkers, mapped tag count, promoter hit rate, RIN score.


Library depth check - Media:Less_than_500000_Q20tags.xls

Human samples with less than 500,000 Q20 mapped tags = 88

  • 18 macrophage samples from Hume Lab
  • 4 MSC adipo samples from Arner Lab
  • 23 K562 samples from Klinken Lab
  • 10 CMP/GMP/PMN samples from Lenarrtson Lab
  • 3 from Khachigian lab
  • 23 commercial primary cells


Mouse samples with less than 500,000 Q20 mapped tags = 11

  • 4 J2E samples from Klinken lab
  • 3 commercial primary cells


Promoter hit rate check (only for samples in release 12 so far) - Media:Less_than_50percent_promoter_rate.xls

Human samples with less than 50% = 30 12 post mortem tissue samples from Kere lab (RNA was degraded) 4 commercial post mortem tissue samples (RNA looks ok) 3 macrophage samples from Hume Lab 2 Saos samples from Summers Lab 3 neuron/neural stem cells – suspect this is biology


Sample labelling check (by clustering and marker gene checks)
Samples were clustered by Kawaji-san

Al manually checked these clusters and marker genes.

Contains lists of putative biomarkers for some of the primary cells and tissue samples.
Eg. STAR is a marker of the adrenal gland.
PAX1 is a marker of Anulus Pulposus Cells
CRTAC1 is a marker of re-differentiated chondrocytes
ISM2 is a marker of chorionic membrane cells

ECSCR and CDH5 are global markers of endothelial cells



SAMPLES for FREEZE CANDIDATE 1 Here are the candidates for the phase 1 datafreeze. All samples listed here will be used for tag cluster generation but only a subset flaged 'INCLUDE' will be used in main paper figures.


  • Media:Human_Freeze1_samples.xls
  • 988 libraries are included for generating DPI clusters
  • 889 of these pass further QC measures of Q20 mapped depth >500,000, RNA integrity and reproducibility, and will be used for motif finding and gene expression figures.


  • Media:Mouse_Freeze1_samples.xls
  • 402 libraries are included for generating DPI clusters
  • 397 of these pass further QC measures of Q20 mapped depth >500,000, RNA integrity and reproducibility, and will be used for motif finding and gene expression figures.



Matched samples for Human and mouse comparisons


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