|
| Status |
Public on Jan 31, 2017 |
| Title |
HP1a_2 |
| Sample type |
SRA |
| |
|
| Source name |
HP1a, Drosophila S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2-DRSC
treatment: untreated
chip antibody: mouse anti-HP1a C1A9 (RRID: AB528276)
|
| Treatment protocol |
For RNAi experiments cells were incubated in serum-free medium containing 10 mg/mL dsRNA. After 1 hr of incubation, the serum-containing medium was supplied. Samples were taken after 7 days. The dsRNA was prepared using the MEGAScript T7 Transcription Kit (Thermo Fisher Scientific) following the manufacturers instructions.
|
| Growth protocol |
S2-DRSC cells were grown at 26 °C in Schneider's Drosophila medium (Invitrogen) supplemented with 10 % fetal calf serum and antibiotics (100 units/mL penicillin and 100 µg/mL streptomycin)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For chromatin immunoprecipitation (ChIP) cells were crosslinked with 1 % formaldehyde for 5 min at room temperature. Upon cell lysis, protease inhibitors and proteasome inhibitor MG-132 (Enzo Life Sciences) were applied. The chromatin was isolated and sheared with adaptive focused acoustics (Covaris) to an average size of 200 base pair (bp). For each ChIP reaction, chromatin isolated from 1-2 x 10e6 cells was incubated with antibodies precoupled to Protein A/G Sepharose.
All libraries were prepared using MicroPlex (Diagenode) or NEBNext (NEB) Library Preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-Seq reads were aligned to the dm3 genome assembly using Bowtie version 2.2.6 excluding Uextra. Only unique mapping reads were kept with samtools version 1.2.
Raw read quality was accessed using FASTQC version 11.5 and reads filtered using FastX version 0.0.13.
Peak calling was performed using HOMER version 4.8 with parameter sets -style factor -size 200 -fragLength 200 -inputFragLength 200.
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files were generated using MACS version 2.1.1. Bed files were generated using HOMER version 4.8.
|
| |
|
| Submission date |
Aug 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel Imhof |
| E-mail(s) |
imhof@lmu.de
|
| Organization name |
Ludwig-Maximilians-University of Munich
|
| Street address |
Großhadernerstr. 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE86106 |
The Drosophila speciation factor HMR localizes to genomic insulator sites |
|
| Relations |
| BioSample |
SAMN05710829 |
| SRA |
SRX2055948 |
