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Sample GSM1000563

Query DataSets for GSM1000563

Status

Public on Sep 10, 2012

Title

CSHL_RnaSeq_Cortex_adult-8wks (superseded by GSE90205)

Sample type

SRA

Source name

Cortex

Organism

Mus musculus

Characteristics

lab: CSHL-m
lab description: Gingeras - Cold Spring Harbor Laboratory
datatype: RnaSeq
datatype description: Sequencing analysis of RNA expression
cell: Cortex
cell organism: mouse
cell description: Cortex
cell sex: U
age: adult-8wks
age description: Adult 8 weeks
age: adult-8wks
age description: Adult 8 weeks
biorep: 6AWC,6BWC
labexpid: LID47032,LID47033
readtype: 2x101D
readtype description: Paired 101 nt directed reads
spikeinpool: Nist14
strain: C57BL/6J
strain description: A substrain of C57BL/6

Biomaterial provider

1)LICR lab; 2)CSHL lab

Growth protocol

Cortex_Gingeras_protocol.pdf

Extracted molecule

polyA RNA

Extraction protocol

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeCshlLongRnaSeq

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

****************************
GSM1000563 record metadata submitted on Sep 10 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90205
****************************

Data processing

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeCshlLongRnaSeq

Submission date

Sep 10, 2012

Last update date

Feb 26, 2020

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 (3)

GSE36025	Long RNA-seq from ENCODE/Cold Spring Harbor Lab
GSE49417	The conserved organization of the human and mouse transcriptomes
GSE49847	A comparative encyclopedia of DNA elements in the mouse genome

Relations

Reanalyzed by

Superseded by

Reanalyzed by

SRA

BioSample

Named Annotation

GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1.bigWig

Named Annotation

GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2.bigWig

Named Annotation

GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1.bigWig

Named Annotation

GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2.bigWig

Supplementary file	Size	Download	File type/resource
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksContigs.bedRnaElements.gz	13.9 Mb	(ftp)(http)	BEDRNAELEMENTS
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksJunctions.bedRnaElements.gz	13.9 Mb	(ftp)(http)	BEDRNAELEMENTS
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1.bigWig	323.5 Mb	(ftp)(http)	BIGWIG
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2.bigWig	313.7 Mb	(ftp)(http)	BIGWIG
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1.bigWig	321.9 Mb	(ftp)(http)	BIGWIG
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2.bigWig	312.7 Mb	(ftp)(http)	BIGWIG
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksSpikeinsRep1.bam	695.9 Mb	(ftp)(http)	BAM
GSM1000563_mm9_wgEncodeCshlLongRnaSeqCortexAdult8wksSpikeinsRep2.bam	878.2 Mb	(ftp)(http)	BAM
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file