## Description

This track shows enrichment of RNA sequence tags generated by high throughput sequencing (RNA-seq) and mapped to the human genome. Double stranded cDNA was synthesized from fragmented PolyA RNA, and the PCR amplified adapter ligated cDNAs, 150-300 nt long, were sequenced using Illumina GA.

This track shows expression data generated as confirmation of the Yale TFBS tracks.

## Display Conventions and Configuration

This is a composite track that contains multiple data types (views). Instructions for configuring composite tracks are here. ENCODE tracks typically contain one or more of the following views:

Signal
  Density graph (wiggle) of signal enrichment based on processed data.
Alignments
  Mappings of short reads to the genome. These are only available as downloadable files.

## Methods

Cells were grown according to the approved ENCODE cell culture protocols. Trizol Reagent (15596-018, Life Tech) was added to the cell pellet and total RNA was extracted using the protocol provided by the manufacturer. PolyA RNA was purified using MicroPoly(A) Purist kit (AM1919, Life Tech) and was fragmented using RNA Fragmentation Reagent (AM8740, Life Tech). Illumina adapters were ligated to double stranded cDNA which were synthesized using reagents from Life Tech (11917-010). PCR amplified adapter ligated cDNA (150-300 bp) was sequenced using Illumina GA. Sequence reads of 27-33 nt long and with 0-2 mismatches were mapped to the genome. From the mapped tags, a signal map of ChIP DNA fragments was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.

## Credits

These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University; Peggy Farnham at UC Davis; and Kevin Struhl at Harvard. Contact: datasubmission@gersteinlab.org.

## References

Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M Dynamic Transcriptomes during Neural Differentiation of Human Embryonic Stem Cells Revealed by Integrating Short, Long, and Paired-end Sequencing. Proc Natl Acad Sci. 2010 March 1 (Epub ahead of publication).

Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, and Snyder M Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci. 2010 Feb 5 (Epub ahead of publication).

Nagalakshmi U, Zhong Wang , Waern K, Shou C, Raha D, Gerstein M, Snyder M The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 6;320(5881):1344-1349.

## Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.