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Sample GSM2343785

Query DataSets for GSM2343785

Status

Public on Nov 08, 2016

Title

total RNA-seq from esophagus squamous epithelium (ENCLB736YFJ)

Sample type

SRA

Source name

Homo sapiens esophagus squamous epithelium tissue female adult (51 year)

Organism

Homo sapiens

Characteristics

tissue_type: esophagus squamous epithelium
biomaterial_type: tissue
description: Esophagus mucosa tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS842VSS (SAMN05897621)
age: 51 year
dev stage: adult
donor_id: ENCDO271OUW
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS842VSS at ENCODE; https://www.encodeproject.org/ENCBS842VSS/
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/24be2f2d-f5d1-4b7f-9231-d078bbba5a92/@@download/attachment/296192.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR510MIA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the mucosa of the esophagus 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: ENCSR510MIA
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB736YFJ
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)

GSE88323

total RNA-seq from esophagus squamous epithelium (ENCSR510MIA)

Relations

BioSample

SAMN05897621

SRA

SRX2244175

Named Annotation

GSM2343785_ENCFF659QLY_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2343785_ENCFF950TDJ_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2343785_ENCFF790EGV_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2343785_ENCFF980ONF_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2343785_ENCFF158QIJ_transcript_quantifications_GRCh38.tsv.gz	7.6 Mb	(ftp)(http)	TSV
GSM2343785_ENCFF186UQB_minus_strand_signal_of_unique_reads_hg19.bigWig	59.9 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF560ZBX_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2343785_ENCFF659QLY_minus_strand_signal_of_all_reads_GRCh38.bigWig	66.0 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF693UMX_transcript_quantifications_hg19.tsv.gz	7.5 Mb	(ftp)(http)	TSV
GSM2343785_ENCFF790EGV_plus_strand_signal_of_unique_reads_GRCh38.bigWig	61.7 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF795PBG_plus_strand_signal_of_all_reads_hg19.bigWig	66.9 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF809VEU_minus_strand_signal_of_all_reads_hg19.bigWig	65.4 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF902LXW_plus_strand_signal_of_unique_reads_hg19.bigWig	61.7 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF944ZJI_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2343785_ENCFF950TDJ_plus_strand_signal_of_all_reads_GRCh38.bigWig	67.6 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCFF980ONF_minus_strand_signal_of_unique_reads_GRCh38.bigWig	59.9 Mb	(ftp)(http)	BIGWIG
GSM2343785_ENCLB736YFJ_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file