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GEO accession:
Sample GSM2192081
Query DataSets for GSM2192081
Status
Public on Jun 22, 2016
Title
total RNA-seq from forebrain (ENCLB214HEI)
Sample type
SRA
Source name
Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (12.5 days)
Organism
Mus musculus
Characteristics
tissue_type: forebrain
biomaterial_type: tissue
description: Forebrain from 68 embryonic 12.5 day mice
biosample encode accession: ENCBS617DPG (SAMN05202060)
age: 12.5 day
donor_id: ENCDO956IXV
dev stage: embryonic
Sex: pooled male and female
health state: healthy
lab: Len Pennacchio, LBNL
link: ENCBS617DPG at ENCODE;
https://www.encodeproject.org/ENCBS617DPG/
link: Derived from ENCODE donor ENCDO956IXV;
https://www.encodeproject.org/ENCDO956IXV/
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: Ambion mirVana
extraction protocol:
https://www.encodeproject.org/documents/f0cc5a7f-96a5-4970-9f46-317cc8e2d6a4/@@download/attachment/cms_055423.pdf,
extraction protocol:
https://www.encodeproject.org/documents/428a184d-7fa1-4599-9d8d-749c2eba7edd/@@download/attachment/cms_055740.pdf,
extraction protocol:
https://www.encodeproject.org/documents/49fd5b3b-9878-4ec8-92bf-ef6dce9116e3/@@download/attachment/SMARTer%20Ultra%20Low%20RNA%20Kit%20for%20Illumina%20Sequencing%20User%20Manual%20%28PT5163-1%29_120213.pdf
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina HiSeq 2500
Description
https://www.encodeproject.org/experiments/ENCSR647QBV/
***************
biological replicate number: 2
technical replicate number: 1
description: e12.5 forebrain
experiment encode accession: ENCSR647QBV
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-05-03
lab: Barbara Wold, Caltech
library encode accession: ENCLB214HEI
size range: >200
spikeins used: /references/ENCSR884LPM/
nucleic acid starting quantity: 10.0
nucleic acid starting quantity units: ng
Data processing
See GSM*_README.txt supplementary file linked below
Submission date
Jun 07, 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
CA
ZIP/Postal code
94305-5120
Country
USA
Platform ID
GPL17021
Series (1)
GSE82852
total RNA-seq from forebrain (ENCSR647QBV)
Relations
BioSample
SAMN05202060
SRA
SRX1833953
Named Annotation
GSM2192081_ENCFF420OST_signal_of_all_reads_mm10.bigWig
Named Annotation
GSM2192081_ENCFF277JCL_signal_of_unique_reads_mm10.bigWig
Supplementary file
Size
Download
File type/resource
GSM2192081_ENCFF186ZME_transcript_quantifications_mm10.tsv.gz
4.5 Mb
(ftp)
(http)
TSV
GSM2192081_ENCFF277JCL_signal_of_unique_reads_mm10.bigWig
199.5 Mb
(ftp)
(http)
BIGWIG
GSM2192081_ENCFF420OST_signal_of_all_reads_mm10.bigWig
225.7 Mb
(ftp)
(http)
BIGWIG
GSM2192081_ENCFF601JPN_gene_quantifications_mm10.tsv.gz
2.1 Mb
(ftp)
(http)
TSV
GSM2192081_ENCLB214HEI_README.txt.gz
638 b
(ftp)
(http)
TXT
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
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