Exon arrays of Roadmap celltypes(line, primary cells, tissues). University of Washington, Stamlab (NREMC)
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EXPERIMENT XML file 'NREMC.experiment.expressionArray.DS16018.xml' uploaded
EXPERIMENT_TYPE: Expression Array
GROWTH_PROTOCOL: Followed vendor recommendations for growth protocol/media
EXTRACT_PROTOCOL: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
LABEL_PROTOCOL: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
HYB_PROTOCOL: Hybridizations were carried out according the manufacturer (Affymetrix) protocol
SCAN_PROTOCOL: Affymterix Gene Chip Scanner 3000
DATA_PROCESSING: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
VALUE_DEFINITION: quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized