|
| Status |
Public on Mar 27, 2013 |
| Title |
Wild Type 10.5 dpp CAGE |
| Sample type |
SRA |
| |
|
| Source name |
testes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testes
developmental stage: 10.5 dpp
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 |
CAGE (cap analysis of gene expression) was as described (Yang et al., 2011)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CAGE libraries were analyzed as follows: After removing adaptor sequences and checking read quality using Flexbar 2.2 with the parameters of “-at 3 -ao 10 --min-readlength 20 --max-uncalled 70 --phred-pre-trim 10”, we retained only reads beginning with NG or GG (the last two nucleotides on the 5′ adaptor). We then removed the first two nucleotides and mapped the sequences to the mouse genome using TopHat 2.0.4. All unique 5′ ends of the mapped positions were considered as CAGE-tag starting sites and grouped into tag clusters using a distance-based method in which the maximal distance between two neighboring tags was required to be <20 bp. The peak position of a tag cluster was then reported as the transcription start site.
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 |
SRX247985 |
| BioSample |
SAMN01943339 |
