Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

ABSTRACT: At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 106 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). Approximately 3ug of total RNA for each cell type was sent to the Center for Array Technology (CAT) for labeling and hybridization to Affymetrix Human Exon 1.0 ST arrays. Briefly, a Whole Transcript Sense Target Labeling Assay (Affymetrix) was used by the CAT to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays. Hybridizations were carried out according the manufacturers protocol. Intensity files from the scanned exon arrays were sent to our lab for analysis at the exon level (Affymetrix ExACT 1.2.1 software). Samples were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Continuing exon profiling of ENCODE approved cell types, these coincide with DNaseI hypersensitivity sequencing assays, ChIP-seq (histone modifications, transcription factors), and other ENCODE assay types.

ORGANISM(S): Homo sapiens

SUBMITTER: UCSC ENCODE DCC

PROVIDER: E-GEOD-19090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Hansen R Scott RS Thomas Sean S Sandstrom Richard R Canfield Theresa K TK Thurman Robert E RE Weaver Molly M Dorschner Michael O MO Gartler Stanley M SM Stamatoyannopoulos John A JA

Proceedings of the National Academy of Sciences of the United States of America 20091204 1

Faithful transmission of genetic material to daughter cells involves a characteristic temporal order of DNA replication, which may play a significant role in the inheritance of epigenetic states. We developed a genome-scale approach--Repli Seq--to map temporally ordered replicating DNA using massively parallel sequencing and applied it to study regional variation in human DNA replication time across multiple human cell types. The method requires as few as 8,000 cytometry-fractionated cells for a ...[more]

PMID: 19966280

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Dataset Information

Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Publications

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

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