GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2344250

Query DataSets for GSM2344250

Status

Public on Nov 08, 2016

Title

total RNA-seq from stomach (ENCLB456EOR)

Sample type

SRA

Source name

Homo sapiens stomach tissue female adult (51 year)

Organism

Homo sapiens

Characteristics

tissue_type: stomach
biomaterial_type: tissue
description: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS038PAI (SAMN05896801)
age: 51 year
dev stage: adult
donor_id: ENCDO271OUW
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS038PAI at ENCODE; https://www.encodeproject.org/ENCBS038PAI/
link: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/6e7d27f1-e025-452b-ab22-348104aa6403/@@download/attachment/296676.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR853WOM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR853WOM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB456EOR
size range: >200
spikeins used: /references/ENCSR156CIL/

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Oct 13, 2016

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

GPL16791

Series (1)

GSE88594

total RNA-seq from stomach (ENCSR853WOM)

Relations

BioSample

SAMN05896801

SRA

SRX2244651

Named Annotation

GSM2344250_ENCFF440SIW_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344250_ENCFF517PFB_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344250_ENCFF500YWQ_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344250_ENCFF344WWU_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344250_ENCFF074OFV_plus_strand_signal_of_unique_reads_hg19.bigWig	19.9 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF094GQC_minus_strand_signal_of_all_reads_hg19.bigWig	21.7 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF155AGD_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2344250_ENCFF344WWU_minus_strand_signal_of_all_reads_GRCh38.bigWig	21.9 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF440SIW_plus_strand_signal_of_all_reads_GRCh38.bigWig	23.1 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF500YWQ_minus_strand_signal_of_unique_reads_GRCh38.bigWig	19.4 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF517PFB_plus_strand_signal_of_unique_reads_GRCh38.bigWig	20.2 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF617PUY_transcript_quantifications_hg19.tsv.gz	7.2 Mb	(ftp)(http)	TSV
GSM2344250_ENCFF645CNL_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2344250_ENCFF694ZJI_transcript_quantifications_GRCh38.tsv.gz	7.3 Mb	(ftp)(http)	TSV
GSM2344250_ENCFF696KNM_plus_strand_signal_of_all_reads_hg19.bigWig	22.3 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCFF836VIP_minus_strand_signal_of_unique_reads_hg19.bigWig	19.1 Mb	(ftp)(http)	BIGWIG
GSM2344250_ENCLB456EOR_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file