Sample QC

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

Library depth checkmedia: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 (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