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Sample GSM2400152

Query DataSets for GSM2400152

Status

Public on Dec 07, 2016

Title

polyA mRNA RNA-seq from H1-hESC (ENCLB555AMA)

Sample type

SRA

Source name

Homo sapiens H1-hESC stem cell male embryo

Organism

Homo sapiens

Characteristics

cell_type: H1-hESC
biomaterial_type: stem cell
description: embryonic stem cells
biosample encode accession: ENCBS731AAA (SAMN06044728)
dev stage: embryonic
Sex: male
donor_id: ENCDO000AAW
age: unknown
health state: healthy
lab: Thomas Gingeras, CSHL
link: ENCBS731AAA at ENCODE; https://www.encodeproject.org/ENCBS731AAA/
link: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/
link: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771
link: ENCODE dbxrefs H1-hESC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-hESC

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/2828ba15-f9d5-4bce-ad3c-0a7f6a18a6e5/@@download/attachment/LID8461.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

Description

https://www.encodeproject.org/experiments/ENCSR000COU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of the human embryonic stem cell line H1-hESC. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COU
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AMA
size range: >200
spikeins used: /references/ENCSR402QNO/

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Nov 22, 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

GPL10999

Series (1)

GSE90225

polyA mRNA RNA-seq from H1-hESC (ENCSR000COU)

Relations

BioSample

SAMN06044728

SRA

SRX2370468

Named Annotation

GSM2400152_ENCFF485AOP_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2400152_ENCFF090ABV_minus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2400152_ENCFF142LNT_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2400152_ENCFF801APS_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2400152_ENCFF045NOY_gene_quantifications_hg19.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2400152_ENCFF090ABV_minus_strand_signal_of_all_reads_GRCh38.bigWig	195.3 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF142LNT_plus_strand_signal_of_all_reads_GRCh38.bigWig	204.5 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF354QYX_plus_strand_signal_of_unique_reads_hg19.bigWig	183.9 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF359YHK_minus_strand_signal_of_all_reads_hg19.bigWig	194.8 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF479AZO_transcript_quantifications_GRCh38.tsv.gz	8.1 Mb	(ftp)(http)	TSV
GSM2400152_ENCFF485AOP_plus_strand_signal_of_unique_reads_GRCh38.bigWig	183.8 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF653XHG_gene_quantifications_GRCh38.tsv.gz	2.7 Mb	(ftp)(http)	TSV
GSM2400152_ENCFF662GOU_transcript_quantifications_hg19.tsv.gz	7.9 Mb	(ftp)(http)	TSV
GSM2400152_ENCFF713JAG_minus_strand_signal_of_unique_reads_hg19.bigWig	173.7 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF801APS_minus_strand_signal_of_unique_reads_GRCh38.bigWig	173.9 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCFF824LWJ_plus_strand_signal_of_all_reads_hg19.bigWig	203.5 Mb	(ftp)(http)	BIGWIG
GSM2400152_ENCLB555AMA_README.txt.gz	1.9 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file