|
| Status |
Public on Mar 17, 2016 |
| Title |
input DNA |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chip antibody: none
|
| Treatment protocol |
S2 cells (2 x 107) were plated in 5 ml of 1x Schneider’s Drosophila medium without FBS in 10-cm dishes. dsRNA of EGFP was added at 26 °C for 6 h, followed by 5 ml of 1x Schneider’s Drosophila medium with 10% FBS. The cells were then incubated for an additional 72 h to allow for turnover of the target mRNA.
|
| Growth protocol |
S2 cells were grown at 26 °C in Schneider’s Drosophila media (Gibco), supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from Mnase digested nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacture’s instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Basecalls performed using Illumina Miseq/Real Time Analysis.
ChIP-seq reads were aligned to the dm6 genome assembly using Burrows-Wheeler Alignment v0.7.5 (BWA) program, with default "aln" and "sames" parameters.
ChIP peaks were called using Model-based Alignment of ChIP-Seq (MACS) program with the following setting: macs, t, treatment_bamfile; c, control_bamfile; bdg; P=0.05
Genome_build: dm6
Supplementary_files_format_and_content: xls files were generated using MACS program and csv files were generated using R-package ChippeakAnno.
|
| |
|
| Submission date |
Sep 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Masamichi Doiguchi |
| E-mail(s) |
doiguch@nagasaki-u.ac.jp
|
| Organization name |
University of Nagasaki
|
| Street address |
Sakamoto 1-12-4
|
| City |
Nagasaki |
| ZIP/Postal code |
852-8523 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16479 |
| Series (1) |
| GSE72666 |
High-throughput sequence data of ChIP performed with anti-SMARCAD1 (ASNA) or anti-CBP actibodies. |
|
| Relations |
| BioSample |
SAMN04027503 |
| SRA |
SRX1179571 |
