|
| Status |
Public on Dec 13, 2020 |
| Title |
piwiKD-Brm-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
OSC
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Drosophila ovarian somatic cell
genotype/variation: piwi 2days knockdown
chip antibody: anti-Brm (gift from Susumu Hirose in NIG, Japan; 10.1242/dev.083246)
|
| Treatment protocol |
DNA was cross-linked with protein of interest using formaldehyde. After immunoprecipitation using the antibody against the protein of interest, DNA was purified by phenol:chloroform extraction.
|
| Growth protocol |
OSCs were grown at 26°C in culture medium prepared from Shields and Sang M3 Insect Medium (Sigma) supplemented with 0.6 mg/mL glutathione, 10% FBS, 10 mU/mL insulin, and 10% fly extract (Saito et al. 2009).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA libraries were raised using SMARTer ThruPLEX DNA-seq Kit (Clontech) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
2 days knockdown
Brm-ChIPseq-processed data file.csv
|
| Data processing |
mapped to dm6 transcriptome by bowtie2 v2.2.4
culculating FPKM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: Brm-ChIPseq-processed data file.csv (file includes FPKM values for each sample)
|
| |
|
| Submission date |
Nov 14, 2018 |
| Last update date |
Dec 13, 2020 |
| Contact name |
Kaoru Sato |
| E-mail(s) |
k_sato@tmig.or.jp
|
| Organization name |
Tokyo Metropolitan Institute of Gerontology
|
| Street address |
35-2 Sakae-cho, Itabashi-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1730015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE108329 |
Piwi suppresses transcription of Brahma-dependent transposons via Maelstrom in ovarian somatic cells |
|
| Relations |
| BioSample |
SAMN10423414 |
| SRA |
SRX5007618 |
