|
| Status |
Public on Jun 11, 2012 |
| Title |
female brain RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
adult brain
|
| Organism |
Monodelphis domestica |
| Characteristics |
tissue: brain
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from opossum brain and liver using Trizol and further purified using QIAGEN RNAEasy mini kit. Library was constructed using strand-specific protocol (Nucleic Acids Res. 2009:e123) with the exception that total RNA was used instead of polyA+ fraction. In the resultant library reads originate on complementary strand relative to source RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using CASAVA versions 1.7.0-1.8.0
Alignment to MonDom5 assembly of Monodelphis domestica genome was performed using BWA 0.5.9rc1 with default parameters.
Genome_build: MonDom5
Supplementary_files_format_and_content: bedGraph files were created from BAM files using genomeCoverageBed (part of bedtools package v. 2.15.0). BAM files were generated using BWA 0.5.9rc1. Only "properly-paired" reads (0x2 SAM flag) were used
|
| |
|
| Submission date |
Mar 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pavel P Khil |
| E-mail(s) |
pk94j@nih.gov
|
| Phone |
301-496-4638
|
| Fax |
(301)-496-9878
|
| Organization name |
NIDDK
|
| Department |
|
| Lab |
Genetics and Biochemistry Branch
|
| Street address |
5 Memorial Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL15381 |
| Series (1) |
| GSE36861 |
Sex-dependent RNA expression in opossum brain and liver. |
|
| Relations |
| SRA |
SRX132008 |
| BioSample |
SAMN00845672 |
