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Sample GSM2344180 Query DataSets for GSM2344180
Status Public on Nov 08, 2016
Title total RNA-seq from embryonic facial prominence (ENCLB247JXW)
Sample type SRA
 
Source name Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)
Organism Mus musculus
Characteristics tissue_type: embryonic facial prominence
biomaterial_type: tissue
description: Craniofacial prominence from 51 embryonic 10.5 day mice
biosample encode accession: ENCBS199YOQ (SAMN05733890)
age: 10.5 day
dev stage: embryonic
donor_id: ENCDO956IXV
Sex: pooled male and female
health state: healthy
lab: Len Pennacchio, LBNL
link: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/
link: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/
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/ENCSR809VYL/
***************
biological replicate number: 2
technical replicate number: 1
description: Total RNA-seq on 10ng of embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR809VYL
assay title: total RNA-seq
assembly: mm10
encode release date: 2016-08-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB247JXW
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 Oct 13, 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)
GSE88554 total RNA-seq from embryonic facial prominence (ENCSR809VYL)
Relations
BioSample SAMN05733890
SRA SRX2244578
Named Annotation GSM2344180_ENCFF830BLT_signal_of_unique_reads_mm10.bigWig
Named Annotation GSM2344180_ENCFF593YMR_signal_of_all_reads_mm10.bigWig

Supplementary file Size Download File type/resource
GSM2344180_ENCFF535QTR_transcript_quantifications_mm10.tsv.gz 4.5 Mb (ftp)(http) TSV
GSM2344180_ENCFF593YMR_signal_of_all_reads_mm10.bigWig 202.6 Mb (ftp)(http) BIGWIG
GSM2344180_ENCFF672DDJ_gene_quantifications_mm10.tsv.gz 2.1 Mb (ftp)(http) TSV
GSM2344180_ENCFF830BLT_signal_of_unique_reads_mm10.bigWig 173.4 Mb (ftp)(http) BIGWIG
GSM2344180_ENCLB247JXW_README.txt.gz 655 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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