GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM958728

Query DataSets for GSM958728

Status

Public on Jul 12, 2012

Title

Caltech_RnaSeq_GM12878_2x75_200

Sample type

SRA

Source name

GM12878

Organism

Homo sapiens

Characteristics

datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
readtype: 2x75
readtype description: Paired 75 nt reads
insertlength: 200
insertlength description: insert length of 200nt
labexpid: 10565,10515
mapalgorithm: TH1014
mapalgorithm description: TopHat v1.0.14
readtype: 2x75
readtype description: Paired 75 nt reads
replicate: 1,2
insertlength: 200
insertlength description: insert length of 200nt
treatment: None
treatment description: No special treatment or protocol applies
labexpid: 10565
mapalgorithm: TH1014
mapalgorithm description: TopHat v1.0.14
readtype: 2x75
readtype description: Paired 75 nt reads
replicate: 1

Biomaterial provider

Coriell

Treatment protocol

None

Growth protocol

GM12878_protocol.pdf

Extracted molecule

polyA RNA

Extraction protocol

Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCaltechRnaSeq

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer

Data processing

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCaltechRnaSeq

Submission date

Jul 10, 2012

Last update date

May 15, 2019

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)

GSE33480

RNA-seq from ENCODE/Caltech

Relations

Reanalyzed by

GSE97211

SRA

SRX159821

BioSample

SAMN01087942

Named Annotation

GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4.bigWig

Named Annotation

GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4.bigWig

Supplementary file	Size	Download	File type/resource
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200ExonsGencV3cRep1V3.gtf.gz	7.7 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200ExonsGencV3cRep2V3.gtf.gz	7.7 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200GeneDeNovoRep1V3.gtf.gz	1.0 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200GeneDeNovoRep2V3.gtf.gz	1.2 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200GeneGencV3cRep1V3.gtf.gz	1.9 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200GeneGencV3cRep2V3.gtf.gz	1.8 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200JunctionsRep1V3.bigBed	5.8 Mb	(ftp)(http)	BIGBED
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200JunctionsRep2V3.bigBed	6.4 Mb	(ftp)(http)	BIGBED
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2.bam	870.7 Mb	(ftp)(http)	BAM
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep1V2.bam.bai.gz	704.2 Kb	(ftp)(http)	BAI
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2.bam	1.3 Gb	(ftp)(http)	BAM
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200SplicesRep2V2.bam.bai.gz	792.7 Kb	(ftp)(http)	BAI
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TSSRep1V3.gtf.gz	3.1 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TSSRep2V3.gtf.gz	3.1 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TranscriptDeNovoRep1V3.gtf.gz	4.2 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TranscriptDeNovoRep2V3.gtf.gz	4.9 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TranscriptGencV3cRep1V3.gtf.gz	13.0 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Il200TranscriptGencV3cRep2V3.gtf.gz	13.1 Mb	(ftp)(http)	GTF
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep1V4.bigWig	209.7 Mb	(ftp)(http)	BIGWIG
GSM958728_hg19_wgEncodeCaltechRnaSeqGm12878R2x75Th1014Il200SigRep2V4.bigWig	302.4 Mb	(ftp)(http)	BIGWIG
SRA Run Selector
Processed data provided as supplementary file
Raw data are available in SRA