|
| Status |
Public on Mar 27, 2013 |
| Title |
Wild Type Adult PAS |
| Sample type |
SRA |
| |
|
| Source name |
testes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testes
developmental stage: Adult
strain: C57BL/6J
genotype: wild-type
|
| Growth protocol |
Mice were maintained and used according to the guidelines of the Institutional Animal Care and Use Committee of the University of Massachusetts Medical School.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PAS-seq libraries (Table S1) were prepared essentially as described (Shepard et al., 2011) and sequenced using a HiSeq 2000 (100 nt read length).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: PAS-Seq
|
| Data processing |
PAS library was analyzed as follows: We first removed adaptors and performed quality control using Flexbar 2.2 (http://sourceforge.net/projects/theflexibleadap) with the parameters “-at 3 -ao 10 --min-readlength 30 --max-uncalled 70 --phred-pre-trim 10.” For reads beginning with GGG including (NGG, NNG or GNG) and ending with three or more adenosines, we removed the first three nucleotides and mapped the remaining sequence with and without the tailing adenosines to the mouse genome using TopHat 2.0.4. We retained only those reads that could be mapped to the genome without the trailing adenosine residues. Genome-mapping reads containing trailing adenosines were regarded as potentially originating from internal priming and thus discarded. The 3′ end of the mapped, retained read was reported as the site of cleavage and polyadenylation.
Genome_build: mm9
Supplementary_files_format_and_content: BED
|
| |
|
| Submission date |
Mar 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Roy |
| Organization name |
Umass Med
|
| Street address |
364 Plantation St
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE44690 |
An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes |
| GSE45048 |
An Ancient Transcription Factor An Ancient Transcription Factor During Early Meiosis in Mouse Testes (PAS-Seq and CAGE) |
|
| Relations |
| SRA |
SRX247987 |
| BioSample |
SAMN01943341 |
