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Sample GSM2344171

Query DataSets for GSM2344171

Status

Public on Nov 08, 2016

Title

total RNA-seq from Peyer's patch (ENCLB272RXA)

Sample type

SRA

Source name

Homo sapiens Peyer's patch tissue male adult (37 years)

Organism

Homo sapiens

Characteristics

tissue_type: Peyer's patch
biomaterial_type: tissue
description: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.
biosample encode accession: ENCBS024TYX (SAMN05896791)
age: 37 year
dev stage: adult
donor_id: ENCDO845WKR
Sex: male
lab: Thomas Gingeras, CSHL
link: ENCBS024TYX at ENCODE; https://www.encodeproject.org/ENCBS024TYX/
link: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/61a90203-9b19-4007-aed2-cd6101ad0cf3/@@download/attachment/296375.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

https://www.encodeproject.org/experiments/ENCSR802HPM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's small intestine 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: ENCSR802HPM
assay title: total RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB272RXA
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)

GSE88549

total RNA-seq from Peyer's patch (ENCSR802HPM)

Relations

BioSample

SAMN05896791

SRA

SRX2244566

Named Annotation

GSM2344171_ENCFF102VMO_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344171_ENCFF925VKS_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2344171_ENCFF722DEX_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2344171_ENCFF398GUP_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2344171_ENCFF102VMO_plus_strand_signal_of_all_reads_GRCh38.bigWig	120.2 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF129CWI_plus_strand_signal_of_unique_reads_hg19.bigWig	110.0 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF187NLN_gene_quantifications_hg19.tsv.gz	2.5 Mb	(ftp)(http)	TSV
GSM2344171_ENCFF210XSV_transcript_quantifications_hg19.tsv.gz	7.6 Mb	(ftp)(http)	TSV
GSM2344171_ENCFF301NUC_plus_strand_signal_of_all_reads_hg19.bigWig	119.2 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF398GUP_minus_strand_signal_of_unique_reads_GRCh38.bigWig	102.5 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF488GDA_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2344171_ENCFF609FNP_minus_strand_signal_of_all_reads_hg19.bigWig	111.0 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF618HHQ_minus_strand_signal_of_unique_reads_hg19.bigWig	103.2 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF722DEX_minus_strand_signal_of_all_reads_GRCh38.bigWig	111.9 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCFF826JMA_transcript_quantifications_GRCh38.tsv.gz	7.7 Mb	(ftp)(http)	TSV
GSM2344171_ENCFF925VKS_plus_strand_signal_of_unique_reads_GRCh38.bigWig	109.2 Mb	(ftp)(http)	BIGWIG
GSM2344171_ENCLB272RXA_README.txt.gz	1.2 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file