|
| Status |
Public on Jun 30, 2016 |
| Title |
Piwi-IP smRNA-seq from Control-KD |
| Sample type |
SRA |
| |
|
| Source name |
Control-KD OSC
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
variation: RNAi EGFP
|
| Treatment protocol |
Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).
|
| Growth protocol |
Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Piwi was immunoprecipitated from confluent OSCs in 9-cm dishes, and Piwi-associated RNA was isolated from the immunopurified complex by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared using NEBNext Small RNA Library Sample Prep Set (New England BioLabs), according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
processed_smRNAseq.txt
|
| Data processing |
Piwi associated small RNA sequencing data was analyzed as described previously (Sato et al., 2015) with slight modifications. Briefly, adapters were removed using Cutadapt to remove the reads without adapter sequences. The reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), with –n 1 option. Length distribution was calculated using genome-mapped reads, and reads in the range of 24-30 nt were used for further analysis. The genome-mapped reads were mapped to Drosophila melanogaster transposon consensus sequences obtained from Repbase (Jurka, 1998), and reads mapped uniquely to the transposon consensus sequence were used to calculate the frequency of piRNAs obtained from each transposon.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).
|
| |
|
| Submission date |
May 13, 2016 |
| 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) |
| GSE81434 |
Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons |
|
| Relations |
| BioSample |
SAMN04999517 |
| SRA |
SRX1760723 |
