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Sample GSM2344101

Query DataSets for GSM2344101

Status

Public on Nov 08, 2016

Title

total RNA-seq from esophagus muscularis mucosa (ENCLB581IKK)

Sample type

SRA

Source name

Homo sapiens esophagus muscularis mucosa tissue male adult (54 years)

Organism

Homo sapiens

Characteristics

tissue_type: esophagus muscularis mucosa
biomaterial_type: tissue
description: Esophagus muscle layer tissue sent from GTEx to the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS730TAX (SAMN05897500)
age: 54 year
dev stage: adult
donor_id: ENCDO451RUA
Sex: male
lab: Thomas Gingeras, CSHL
link: ENCBS730TAX at ENCODE; https://www.encodeproject.org/ENCBS730TAX/
link: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/09d44fd8-0655-4ca2-a0ce-ae6a6c401eac/@@download/attachment/296292.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR750ETS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's esophagal muscle 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: ENCSR750ETS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB581IKK
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)

GSE88509

total RNA-seq from esophagus muscularis mucosa (ENCSR750ETS)

Relations

BioSample

SAMN05897500

SRA

SRX2244494

Named Annotation

GSM2344101_ENCFF853ZSA_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344101_ENCFF134RAK_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344101_ENCFF553RGA_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344101_ENCFF391EKX_plus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344101_ENCFF084ORQ_transcript_quantifications_hg19.tsv.gz	7.6 Mb	(ftp)(http)	TSV
GSM2344101_ENCFF107JVZ_transcript_quantifications_GRCh38.tsv.gz	7.7 Mb	(ftp)(http)	TSV
GSM2344101_ENCFF134RAK_plus_strand_signal_of_unique_reads_GRCh38.bigWig	97.8 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF391EKX_plus_strand_signal_of_all_reads_GRCh38.bigWig	106.6 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF413HMS_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2344101_ENCFF451YKO_minus_strand_signal_of_unique_reads_hg19.bigWig	93.4 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF553RGA_minus_strand_signal_of_all_reads_GRCh38.bigWig	100.1 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF650KLZ_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2344101_ENCFF681HYE_minus_strand_signal_of_all_reads_hg19.bigWig	99.4 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF853ZSA_minus_strand_signal_of_unique_reads_GRCh38.bigWig	93.4 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF927AAU_plus_strand_signal_of_all_reads_hg19.bigWig	103.4 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCFF978ZUX_plus_strand_signal_of_unique_reads_hg19.bigWig	97.8 Mb	(ftp)(http)	BIGWIG
GSM2344101_ENCLB581IKK_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file