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Sample GSM605626

Query DataSets for GSM605626

Status

Public on Oct 08, 2010

Title

Gingeras_prostate_cell

Sample type

SRA

Source name

prostate

Organism

Homo sapiens

Characteristics

lab: CSHL
lab description: Gingeras - Cold Spring Harbor Laboratory
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell: prostate
cell organism: human
cell description: prostate tissue purchased for CSHL project
cell lineage: endoderm
localization: cell
localization description: Whole cell
protocol: TAP-Only
protocol description: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.
rnaextract: shortTotal
rnaextract description: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation
biorep: gen0161WC
labexpid: crg-61
labversion: Produced by Hannon Lab

Biomaterial provider

ATCC

Growth protocol

Prostate_Gingeras_protocol.pdf

Extracted molecule

total RNA

Extraction protocol

hg18: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCshlShortRnaSeq
hg19: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer

Data processing

hg18: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeCshlShortRnaSeq
hg19: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq

Submission date

Oct 06, 2010

Last update date

Aug 26, 2014

Contact name

ENCODE DCC

E-mail(s)

encode-help@lists.stanford.edu

Organization name

ENCODE DCC

Street address

300 Pasteur Dr

City

Stanford

State/province

ZIP/Postal code

94305-5120

Country

USA

Platform ID

GPL9052

Series (1)

GSE24565

Small RNA-seq from ENCODE/Cold Spring Harbor Lab

Relations

BioSample

SAMN02195960

Named Annotation

GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw.bigWig

Named Annotation

GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw.bigWig

Supplementary file	Size	Download	File type/resource
GSM605626_hg18_wgEncodeCshlShortRnaSeqAlignmentsProstateCellShort.tagAlign.txt.gz	30.4 Mb	(ftp)(http)	TXT
GSM605626_hg18_wgEncodeCshlShortRnaSeqTransfragsProstateCellShort.broadPeak.txt.gz	13.4 Mb	(ftp)(http)	TXT
GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellShortTransfrags.shortFrags.txt.gz	3.7 Mb	(ftp)(http)	TXT
GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellTotalAln.bam	98.0 Mb	(ftp)(http)	BAM
GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellTotalMinusRaw.bigWig	30.4 Mb	(ftp)(http)	BIGWIG
GSM605626_hg19_wgEncodeCshlShortRnaSeqProstateCellTotalPlusRaw.bigWig	30.4 Mb	(ftp)(http)	BIGWIG
Raw data provided as supplementary file
Processed data provided as supplementary file