|
| Status |
Public on Nov 20, 2014 |
| Title |
MIWI IP Miwi ADH/- 1 |
| Sample type |
SRA |
| |
|
| Source name |
Late spermatocyte
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Miwi ADH/-
cell type: late spermatocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent from testes or FACS-purified cells.
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ribosomal RNA minus
|
| Data processing |
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [MIWI IP Miwi ADH/- RPKM] [MIWI IP Miwi +/- RPKM] [MIWI IP Miwi -/- RPKM] [Input Miwi ADH/- RPKM] [Input Miwi +/- RPKM] [Input Miwi -/- RPKM]
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiaki Watanabe |
| E-mail(s) |
toshwatatoshiakiwatanabe@gmail.com
|
| Phone |
81-55-981-6796
|
| Organization name |
Yale University
|
| Street address |
10 Amistad
|
| City |
NewHaven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE42004 |
Spermatogenesis |
| GSE62416 |
Transcriptome analysis in mouse late spermatocyte deficient in pachytene piRNAs (MIWI-immunoprecipitated RNAs) |
|
| Relations |
| BioSample |
SAMN03112981 |
| SRA |
SRX734294 |
