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Sample GSM2072398

Query DataSets for GSM2072398

Status

Public on Mar 18, 2016

Title

total RNA-seq from spinal cord (ENCLB200ZZZ)

Sample type

SRA

Source name

Homo sapiens spinal cord tissue female fetal (24 weeks)

Organism

Homo sapiens

Characteristics

tissue_type: spinal cord
biomaterial_type: tissue
description: Human fetal spinal cord
biosample encode accession: ENCBS072RNA (SAMN04284308)
age: 24 week
donor_id: ENCDO067AAA
dev stage: fetal
Sex: female
lab: Thomas Gingeras, CSHL
link: ENCBS072RNA at ENCODE; https://www.encodeproject.org/ENCBS072RNA/
link: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/
link: data sheet; https://www.encodeproject.org/documents/9f06f639-6fe2-4daf-9ae1-a5bee4c23cf3/@@download/attachment/B608423.pdf
link: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244234-10

Extracted molecule

total RNA

Extraction protocol

data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3aa98cba-81d7-4cec-abd6-f31268ea69e1/@@download/attachment/SID38161.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

https://www.encodeproject.org/experiments/ENCSR000AFH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal spinal cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AFH
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB200ZZZ
size range: >200
spikeins used: /references/ENCSR470JZL/

Data processing

See GSM*_README.txt supplementary file linked below

Submission date

Feb 25, 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

GPL11154

Series (1)

GSE78575

total RNA-seq from spinal cord (ENCSR000AFH)

Relations

SRA

SRX1603434

BioSample

SAMN04284308

Named Annotation

GSM2072398_ENCFF505UJX_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2072398_ENCFF326XMS_plus_strand_signal_of_all_reads_GRCh38.bigWig

Named Annotation

GSM2072398_ENCFF940WOT_plus_strand_signal_of_unique_reads_GRCh38.bigWig

Named Annotation

GSM2072398_ENCFF657OYB_minus_strand_signal_of_all_reads_GRCh38.bigWig

Supplementary file	Size	Download	File type/resource
GSM2072398_ENCFF032WPQ_minus_strand_signal_of_all_reads_hg19.bigWig	343.5 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF038HYA_transcript_quantifications_hg19.tsv.gz	7.9 Mb	(ftp)(http)	TSV
GSM2072398_ENCFF084PQR_gene_quantifications_hg19.tsv.gz	2.6 Mb	(ftp)(http)	TSV
GSM2072398_ENCFF124HBY_minus_strand_signal_of_unique_reads_hg19.bigWig	330.0 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF126UNL_gene_quantifications_GRCh38.tsv.gz	2.7 Mb	(ftp)(http)	TSV
GSM2072398_ENCFF251AWD_transcript_quantifications_GRCh38.tsv.gz	8.0 Mb	(ftp)(http)	TSV
GSM2072398_ENCFF326XMS_plus_strand_signal_of_all_reads_GRCh38.bigWig	383.3 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF499PBL_plus_strand_signal_of_all_reads_hg19.bigWig	357.9 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF505UJX_minus_strand_signal_of_unique_reads_GRCh38.bigWig	346.1 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF621WAT_minus_strand_signal_of_unique_reads_hg19.bigWig	347.5 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF657OYB_minus_strand_signal_of_all_reads_GRCh38.bigWig	367.5 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF685FSA_plus_strand_signal_of_all_reads_hg19.bigWig	382.4 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF723FAK_plus_strand_signal_of_unique_reads_hg19.bigWig	363.3 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF785AFH_plus_strand_signal_of_unique_reads_hg19.bigWig	345.3 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF797VHJ_minus_strand_signal_of_all_reads_hg19.bigWig	367.9 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCFF940WOT_plus_strand_signal_of_unique_reads_GRCh38.bigWig	362.1 Mb	(ftp)(http)	BIGWIG
GSM2072398_ENCLB200ZZZ_README.txt.gz	1.3 Kb	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file