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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.
Project News:
2010/9/28:
EXPERIMENT XML file 'NREMC.experiment.expressionArray.DS13229.xml' uploaded
alias: DS13229-exon
center_name: NREMC
STUDY_REF: UwStam_NREMC_CA
SAMPLE_DESCRIPTOR: IMR90
ATTRIBUTES
EXPERIMENT_TYPE: Expression Array
PLATFORM: GPL5188
GROWTH_PROTOCOL: Followed vendor recommendations for growth protocol/media
TREATMENT_PROTOCOL: None
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
PROBE_GROUP_FILE: HuEx-1_0-st-v2.r2.pgf
META-PROBESET_FILE: None
VALUE_DEFINITION: quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
center_name: NREMC
STUDY_REF: UwStam_NREMC_CA
SAMPLE_DESCRIPTOR: IMR90
ATTRIBUTES
EXPERIMENT_TYPE: Expression Array
PLATFORM: GPL5188
GROWTH_PROTOCOL: Followed vendor recommendations for growth protocol/media
TREATMENT_PROTOCOL: None
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
PROBE_GROUP_FILE: HuEx-1_0-st-v2.r2.pgf
META-PROBESET_FILE: None
VALUE_DEFINITION: quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
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