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Sample GSM2343705

Query DataSets for GSM2343705

Status

Public on Nov 08, 2016

Title

total RNA-seq from breast epithelium (ENCLB197GXK)

Sample type

SRA

Source name

Homo sapiens breast epithelium tissue female adult (51 year)

Organism

Homo sapiens

Characteristics

tissue_type: breast epithelium
biomaterial_type: tissue
description: Mammary breast tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS160KYO (SAMN05896927)
age: 51 year
dev stage: adult
donor_id: ENCDO271OUW
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS160KYO at ENCODE; https://www.encodeproject.org/ENCBS160KYO/
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/5347ecf9-4def-48be-ac30-e5a84a473dbc/@@download/attachment/296318.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR438YPF/
***************
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 adipose 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: ENCSR438YPF
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB197GXK
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)

GSE88273

total RNA-seq from breast epithelium (ENCSR438YPF)

Relations

BioSample

SAMN05896927

SRA

SRX2244089

Named Annotation

GSM2343705_ENCFF874ALU_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2343705_ENCFF180EHY_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2343705_ENCFF756GRG_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2343705_ENCFF428NBV_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2343705_ENCFF082SUT_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2343705_ENCFF099FUF_transcript_quantifications_GRCh38.tsv.gz	7.9 Mb	(ftp)(http)	TSV
GSM2343705_ENCFF154WCI_plus_strand_signal_of_unique_reads_hg19.bigWig	243.8 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF159SXT_plus_strand_signal_of_all_reads_hg19.bigWig	256.2 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF180EHY_plus_strand_signal_of_all_reads_GRCh38.bigWig	257.8 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF428NBV_plus_strand_signal_of_unique_reads_GRCh38.bigWig	244.1 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF467GZM_minus_strand_signal_of_unique_reads_hg19.bigWig	239.9 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF500GZL_minus_strand_signal_of_all_reads_hg19.bigWig	253.8 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF557XAK_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2343705_ENCFF756GRG_minus_strand_signal_of_unique_reads_GRCh38.bigWig	240.5 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCFF777ERL_transcript_quantifications_hg19.tsv.gz	7.8 Mb	(ftp)(http)	TSV
GSM2343705_ENCFF874ALU_minus_strand_signal_of_all_reads_GRCh38.bigWig	255.2 Mb	(ftp)(http)	BIGWIG
GSM2343705_ENCLB197GXK_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file