|
Status |
Public on Dec 01, 2011 |
Title |
F1 E17.5 Brain RNA-seq Cross 2 (CxB) |
Sample type |
SRA |
|
|
Source name |
Whole Brain
|
Organism |
Mus musculus |
Characteristics |
strain: Hybrid: F1 from CastEi/J mother x C57BL/6J 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 |
E-mail(s) |
brian.deveale@utoronto.ca
|
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 |
|
Relations |
SRA |
SRX054613 |
BioSample |
SAMN00254197 |