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Sample GSM2072579

Query DataSets for GSM2072579

Status

Public on Mar 18, 2016

Title

total RNA-seq from forebrain (ENCLB472TKY)

Sample type

SRA

Source name

Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

Organism

Mus musculus

Characteristics

tissue_type: forebrain
biomaterial_type: tissue
description: Forebrain from 15 postnatal 0 day mice
biosample encode accession: ENCBS038AAA (SAMN04283981)
age: 0 day
donor_id: ENCDO469XMJ
dev stage: postnatal
Sex: pooled male and female
health state: healthy
lab: Len Pennacchio, LBNL
link: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/
link: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/
link: excision protocol; https://www.encodeproject.org/documents/631aa21c-8e48-467e-8cac-d40c875b3913/@@download/attachment/StandardTissueExcisionProtocol_02132017.pdf

Extracted molecule

total RNA

Extraction protocol

extraction method: see document
general protocol: https://www.encodeproject.org/documents/df23959e-a00f-488b-a1a3-4c4f391d69eb/@@download/attachment/LID292122.pdf

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

https://www.encodeproject.org/experiments/ENCSR723SZV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent isolates of forebrain tissue. They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR723SZV
assay title: total RNA-seq
assembly: mm10
encode release date: 2014-09-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB472TKY
size range: >200
spikeins used: /references/ENCSR156CIL/

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

GPL13112

Series (1)

GSE78667

total RNA-seq from forebrain (ENCSR723SZV)

Relations

SRA

SRX1603639

BioSample

SAMN04283981

Named Annotation

GSM2072579_ENCFF512MHA_plus_strand_signal_of_unique_reads_mm10.bigWig

Named Annotation

GSM2072579_ENCFF516SHM_minus_strand_signal_of_unique_reads_mm10.bigWig

Named Annotation

GSM2072579_ENCFF189OVG_minus_strand_signal_of_all_reads_mm10.bigWig

Named Annotation

GSM2072579_ENCFF982BUS_plus_strand_signal_of_all_reads_mm10.bigWig

Supplementary file	Size	Download	File type/resource
GSM2072579_ENCFF189OVG_minus_strand_signal_of_all_reads_mm10.bigWig	156.0 Mb	(ftp)(http)	BIGWIG
GSM2072579_ENCFF512MHA_plus_strand_signal_of_unique_reads_mm10.bigWig	143.4 Mb	(ftp)(http)	BIGWIG
GSM2072579_ENCFF516SHM_minus_strand_signal_of_unique_reads_mm10.bigWig	143.8 Mb	(ftp)(http)	BIGWIG
GSM2072579_ENCFF896FWG_transcript_quantifications_mm10.tsv.gz	4.3 Mb	(ftp)(http)	TSV
GSM2072579_ENCFF976DIF_gene_quantifications_mm10.tsv.gz	1.9 Mb	(ftp)(http)	TSV
GSM2072579_ENCFF982BUS_plus_strand_signal_of_all_reads_mm10.bigWig	156.0 Mb	(ftp)(http)	BIGWIG
GSM2072579_ENCLB472TKY_README.txt.gz	753 b	(ftp)(http)	TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file