|
| Status |
Public on Jun 05, 2015 |
| Title |
YbCLIP in OSCs - rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovarian Somatic Cells (OSC), Yb CLIP
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: OSC
cell type: ovarian somatic cell line
variation: untreated
ip antibody: Yb antibody (Murota et al., 2014)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For CLIP, anti-Yb antibody (Murota et al., 2014 [PMID 24953657]) was used to immunopurify Yb from OSC after irradiation by UV (254 nm) for crosslinking. RNAs within the immunoprecipitates were extracted for library construction as described previously (Murota et al., 2014).
For CLIP-seq, library was constructed as described previously (Murota et al., 2014).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
OSC cell line is described in Saito et al., Nature 2009 [PMID 19812547]
|
| Data processing |
Library strategy: CLIP-Seq
For YbCLIP tags, reads were processed as described previously (Murota et al., 2014).
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: CLIP-seq: Unique CLIP tag sequences with length in the range of 30-50nt.
Supplementary_files_format_and_content: Piwi-associated small RNA-seq (RIP-seq): Small RNA sequences and their read counts for small RNAs with length in the range of 20-30nt and have read count over 100.
|
| |
|
| Submission date |
Jun 05, 2015 |
| Last update date |
Jul 03, 2021 |
| Contact name |
Yuka W. Iwasaki |
| E-mail(s) |
iwasaki@keio.jp
|
| Organization name |
Keio University School of Medicine
|
| Department |
Department of Molecular Biology
|
| Lab |
Siomi Lab
|
| Street address |
35 Shinanomachi, Shinjuku-ku,
|
| City |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE69625 |
Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb |
|
| Relations |
| BioSample |
SAMN03764039 |
| SRA |
SRX1051751 |
