GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2344087

Query DataSets for GSM2344087

Status

Public on Nov 08, 2016

Title

total RNA-seq from gastroesophageal sphincter (ENCLB414WBQ)

Sample type

SRA

Source name

Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

Organism

Homo sapiens

Characteristics

tissue_type: gastroesophageal sphincter
biomaterial_type: tissue
description: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS616IQR (SAMN05897374)
age: 53 year
dev stage: adult
donor_id: ENCDO793LXB
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS616IQR at ENCODE; https://www.encodeproject.org/ENCBS616IQR/
link: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/a2dface5-1cb1-4d04-83ea-8b72997ec14f/@@download/attachment/296189.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR740YMS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections from the esophagogastric junction 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: ENCSR740YMS
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-02-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB414WBQ
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)

GSE88501

total RNA-seq from gastroesophageal sphincter (ENCSR740YMS)

Relations

BioSample

SAMN05897374

SRA

SRX2244504

Named Annotation

GSM2344087_ENCFF461YEE_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344087_ENCFF203IBV_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344087_ENCFF373KTQ_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344087_ENCFF970UKB_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344087_ENCFF203IBV_minus_strand_signal_of_unique_reads_GRCh38.bigWig	52.1 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF251EBM_minus_strand_signal_of_unique_reads_hg19.bigWig	52.0 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF296EYT_plus_strand_signal_of_all_reads_hg19.bigWig	56.3 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF373KTQ_plus_strand_signal_of_unique_reads_GRCh38.bigWig	53.3 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF440IKM_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2344087_ENCFF461YEE_plus_strand_signal_of_all_reads_GRCh38.bigWig	57.0 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF603QTK_plus_strand_signal_of_unique_reads_hg19.bigWig	53.3 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF749AJA_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2344087_ENCFF815MRJ_transcript_quantifications_GRCh38.tsv.gz	7.6 Mb	(ftp)(http)	TSV
GSM2344087_ENCFF835OBP_transcript_quantifications_hg19.tsv.gz	7.5 Mb	(ftp)(http)	TSV
GSM2344087_ENCFF970UKB_minus_strand_signal_of_all_reads_GRCh38.bigWig	55.7 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCFF981ICB_minus_strand_signal_of_all_reads_hg19.bigWig	55.0 Mb	(ftp)(http)	BIGWIG
GSM2344087_ENCLB414WBQ_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file