|
| Status |
Public on Feb 10, 2013 |
| Title |
Embryonic4 |
| Sample type |
SRA |
| |
|
| Source name |
cerebral cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E17
tissue: cerebral cortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
trizol extraction for RNA standard illumina RS-100-0801 mRNA-Seq 8 sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7.1
alignment: tophat (v1.0.13) and bowtie (v0.12.7.0)
read counts: HT-SEQ (0.5.3p3)
normalization and differential expression: DE-SEQ (v1.6.1)
variant base calls: SAMtools pileup (samtools-0.1.7a)
Genome_build: mm9
Supplementary_files_format_and_content: variance stabalized quantified data, DE-Seq normalized values
|
| |
|
| Submission date |
Aug 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
J Raphael Gibbs |
| E-mail(s) |
gibbsr@mail.nih.gov
|
| Organization name |
National Institutue on Aging, NIH
|
| Department |
Computational Biology Core
|
| Lab |
Laboratory of Neurogenetics
|
| Street address |
35 Convent Drive, Bldg 35/1A1015, MSC3707
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE39866 |
A comprehensive view of the transcriptome during development of the mouse cerebral cortex |
|
| Relations |
| SRA |
SRX172887 |
| BioSample |
SAMN01096594 |
