Sample QC
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-differentiation chondrocytes
