GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2343179

Query DataSets for GSM2343179

Status

Public on Nov 08, 2016

Title

total RNA-seq from uterus (ENCLB929UGW)

Sample type

SRA

Source name

Homo sapiens uterus tissue female adult (51 year)

Organism

Homo sapiens

Characteristics

tissue_type: uterus
biomaterial_type: tissue
description: Uterus aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS887WTT (SAMN05897667)
dev stage: adult
Sex: female
donor_id: ENCDO271OUW
age: 51 year
lab: Thomas Gingeras, CSHL
link: ENCBS887WTT at ENCODE; https://www.encodeproject.org/ENCBS887WTT/
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/0836e1fe-b257-4569-accf-2da13c5ef119/@@download/attachment/296672.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR071ZLM/
***************
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 uterus 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: ENCSR071ZLM
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-04
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB929UGW
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)

GSE88005

total RNA-seq from uterus (ENCSR071ZLM)

Relations

BioSample

SAMN05897667

SRA

SRX2244920

Named Annotation

GSM2343179_ENCFF724ZJB_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2343179_ENCFF687IWQ_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2343179_ENCFF111GUA_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2343179_ENCFF827USX_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2343179_ENCFF111GUA_minus_strand_signal_of_unique_reads_GRCh38.bigWig	31.1 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF190VLV_minus_strand_signal_of_unique_reads_hg19.bigWig	31.1 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF278CKI_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2343179_ENCFF311GFL_minus_strand_signal_of_all_reads_hg19.bigWig	33.6 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF315DBK_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2343179_ENCFF447ZQL_transcript_quantifications_hg19.tsv.gz	7.3 Mb	(ftp)(http)	TSV
GSM2343179_ENCFF497MII_plus_strand_signal_of_unique_reads_hg19.bigWig	32.2 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF630DFX_plus_strand_signal_of_all_reads_hg19.bigWig	34.9 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF687IWQ_plus_strand_signal_of_unique_reads_GRCh38.bigWig	32.2 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF724ZJB_plus_strand_signal_of_all_reads_GRCh38.bigWig	35.4 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF827USX_minus_strand_signal_of_all_reads_GRCh38.bigWig	33.7 Mb	(ftp)(http)	BIGWIG
GSM2343179_ENCFF903JDJ_transcript_quantifications_GRCh38.tsv.gz	7.4 Mb	(ftp)(http)	TSV
GSM2343179_ENCLB929UGW_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file