|
| Status |
Public on Jan 31, 2013 |
| Title |
adult testis small RNAs |
| Sample type |
SRA |
| |
|
| Source name |
adult testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: testis
|
| Treatment protocol |
sperm was treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H 2 O) for 20 min on ice to eliminate somatic cell contamination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
small RNA was ligated sequentially to 5'- and 3'-adapters, followed by RT-PCR to producethe sequencing library. The PCR products were purified and sequenced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Data cleaning and length distribution: 1) Getting rid of low quality reads 2) Getting rid of reads with 5' primer contaminants 3) Getting rid of reads without 3' primer 4) Getting rid of reads without the insert tag 5) Getting rid of reads with poly A 6) Getting rid of reads shorter than 18nt 7) Summarize the length distribution of the clean reads
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome (build mm9).
Genome_build: mm9
Supplementary_files_format_and_content: text files containing the reads number of each sequence
|
| |
|
| Submission date |
Jun 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Chen |
| E-mail(s) |
qichen.ioz@gmail.com
|
| Phone |
86-10-64807182
|
| Organization name |
INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES
|
| Department |
State Key Laboratory of Reproductive Biology
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE38702 |
small RNA deep-sequencing of mature sperm, testis and uterus in mice |
|
| Relations |
| SRA |
SRX154530 |
| BioSample |
SAMN01048219 |
