Sample QC: Difference between revisions
Al Forrest (talk | contribs) No edit summary |
Al Forrest (talk | contribs) No edit summary |
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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. |
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*18 macrophage samples from Hume Lab |
*18 macrophage samples from Hume Lab |
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*23 commercial primary cells |
*23 commercial primary cells |
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Mouse samples with less than 500,000 Q20 mapped tags = '''11''' |
Mouse samples with less than 500,000 Q20 mapped tags = '''11''' |
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*3 commercial primary cells |
*3 commercial primary cells |
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Samples were clustered by Kawaji-san |
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Al manually checked these clusters and marker genes. |
Al manually checked these clusters and marker genes. |
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Contains lists of putative biomarkers for some of the primary cells and tissue samples.<br> |
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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> |
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[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr20:21683715..21699200 PAX1] is a marker of Anulus Pulposus Cells<br> |
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[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr10:99583300..99832041 CRTAC1] is a marker of re-differentiated chondrocytes<br> |
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[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=0y8YpvmVMhCuUpRudIaxlC;loc=hg19::chr14:77934618..77971327 ISM2] is a marker of chorionic membrane cells<br> |
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| ⚫ | [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> |
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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> |
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| ⚫ | [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> |
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'''SAMPLES for FREEZE CANDIDATE 1''' |
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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. |
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*[[Media:Human_Freeze1_samples.xls]] |
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*[[Media:Mouse_Freeze1_samples.xls]] |
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Revision as of 17:36, 7 December 2011
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.
- 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.
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.
