|
| Status |
Public on Jun 30, 2016 |
| Title |
HP1a ChIP-seq from Control-KD sample1 |
| Sample type |
SRA |
| |
|
| Source name |
Control-KD OSC
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Ovarian Somatic Cells (OSC)
variation: RNAi EGFP
chip antibody: anti-HP1a antibody (C1A9, DSHB)
|
| 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 |
genomic DNA |
| Extraction protocol |
OSC cells were fixed, lysed, and their nuclei isolated using truChIP Chromatin Shearing Kits (Covaris) according to the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), then diluted with ChIP buffer. IP was performed using 3 μg of antibodies on Dynabeads-Protein G beads. Samples were reverse cross-linked, treated with RNase and Proteinase K, and DNA was extracted.
DNA fragments from the ChIP experiment were sheared to ~200 bases using Covaris S220 (Covaris), and were used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
processed_HP1ChIPseq.txt
|
| Data processing |
Adapters were removed from the ChIP-seq reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), using --M 1 --best --strata parameters. Reads mapped to the genome were extracted and mapped to Drosophila melanogaster transposon consensus sequences from Repbase (Jurka, 1998), permitting up to three mismatches and extracting those that mapped uniquely to the transposon consensus sequence.
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 |
SAMN04999496 |
| SRA |
SRX1760702 |
