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Sample GSM665476 Query DataSets for GSM665476
Status Public on Dec 01, 2011
Title F1 E17.5 Brain RNA-seq Cross 1 (BxC)
Sample type SRA
Source name Whole Brain
Organism Mus musculus
Characteristics strain: Hybrid: F1 from C57BL/6J mother x CastEi/J father
age: E17.5
Treatment protocol Samples were snap chilled with liquid nitrogen immediately after dissection
Growth protocol Breeding pairs were fed ad libitum on standard chow
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol followed by mRNA purification with dynabeads. Double stranded cDNA libraries were made using the Illumina mRNA-Seq kit according to the manufacturer's recommendations (Illumina) and converted into libraries (adapter ligation, PCR, cleanup) using a NEBNext kit according to the manufacturer's recommendations (NEB). Libraries were verified on an Agilent Bioanalyzer and by qRT-PCR before sequencing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Dynabead mRNA Extraction following total RNA extraction with Trizol
Data processing Alignment: Sequence reads were mapped to mouse genome (July 2007 NCBI 37/mm9) and a collection of all known and predicted splice junctions (Babak et al. 2010) using Novoalign. All uniquely aligning reads were retained for analysis.
Submission date Feb 02, 2011
Last update date May 15, 2019
Contact name Brian DeVeale
Phone 4164587631
Fax 4169782666
Organization name University of Toronto
Department Molecular Genetics
Lab Derek van der Kooy
Street address 160 College Street, rm 1110
City Toronto
State/province Ontario
ZIP/Postal code M5S3E1
Country Canada
Platform ID GPL13112
Series (1)
GSE27016 Estimates of total imprint number withstand transcriptome test
SRA SRX054612
BioSample SAMN00254196

Supplementary file Size Download File type/resource
GSM665476_bxc1.bed.gz 477.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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