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Sample GSM2071298

Query DataSets for GSM2071298

Status

Public on Mar 18, 2016

Title

single cell RNA-seq from GM12878 (ENCLB198OUV)

Sample type

SRA

Source name

Homo sapiens GM12878 immortalized cell line

Organism

Homo sapiens

Characteristics

line: GM12878
biomaterial_type: immortalized cell line
description: Single GM12878 cell, part of a set of 10
biosample encode accession: ENCBS950FXN (SAMN04284507)
age: unknown
dev stage: adult
Sex: female
health state: unknown
lab: Barbara Wold, Caltech
link: ENCBS950FXN at ENCODE; https://www.encodeproject.org/ENCBS950FXN/
link: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/
link: growth protocol; https://www.encodeproject.org/documents/1bb75b62-ac29-4368-9855-68d410e1963a/@@download/attachment/GM12878_protocol.pdf
link: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526
link: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166

Extracted molecule

total RNA

Extraction protocol

general protocol: https://www.encodeproject.org/documents/e3110414-4013-425e-94f6-72c549702bde/@@download/attachment/Supplemental_Material.pdf
extraction method: None

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

https://www.encodeproject.org/experiments/ENCSR000AJA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq of a single GM12878 cell
experiment encode accession: ENCSR000AJA
assay title: single cell RNA-seq
assembly: GRCh38, hg19
possible controls: ENCSR673UIY
encode release date: 2014-06-30
lab: Barbara Wold, Caltech
library encode accession: ENCLB198OUV
size range: >200
spikeins used: /references/ENCSR013YHQ/
nucleic acid starting quantity: 1
nucleic acid starting quantity units: cells

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Feb 24, 2016

Last update date

May 15, 2019

Contact name

ENCODE DCC

E-mail(s)

[email protected]

Organization name

ENCODE DCC

Street address

300 Pasteur Dr

City

Stanford

State/province

ZIP/Postal code

94305-5120

Country

USA

Platform ID

GPL11154

Series (1)

GSE78308

single cell RNA-seq from GM12878 (ENCSR000AJA)

Relations

SRA

SRX1602997

BioSample

SAMN04284507

Named Annotation

GSM2071298_ENCFF502UPM_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2071298_ENCFF474SZZ_signal_of_unique_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2071298_ENCFF058MJO_signal_of_all_reads_hg19.bigWig	27.1 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF151OPU_transcript_quantifications_hg19.tsv.gz	6.7 Mb	(ftp)(http)	TSV
GSM2071298_ENCFF154RSV_transcript_quantifications_GRCh38.tsv.gz	6.8 Mb	(ftp)(http)	TSV
GSM2071298_ENCFF159DWS_signal_of_all_reads_hg19.bigWig	24.7 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF474SZZ_signal_of_unique_reads_GRCh38.bigWig	21.1 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF502UPM_signal_of_all_reads_GRCh38.bigWig	27.2 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF567PSN_signal_of_unique_reads_hg19.bigWig	20.2 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF641ALS_signal_of_unique_reads_hg19.bigWig	21.1 Mb	(ftp)(http)	BIGWIG
GSM2071298_ENCFF649FHZ_gene_quantifications_GRCh38.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2071298_ENCFF847JJW_gene_quantifications_hg19.tsv.gz	2.4 Mb	(ftp)(http)	TSV
GSM2071298_ENCLB198OUV_README.txt.gz	981 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file