|
| Status |
Public on Apr 30, 2014 |
| Title |
Pol2_WT |
| Sample type |
SRA |
| |
|
| Source name |
wild-type cells - anti-RNAPII
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: Late embryonic derived S2 cells
cell line: S2 Schneider cells
|
| Treatment protocol |
S2 cells were treated with formaldehyde followed by standard sonication procedures
|
| Growth protocol |
S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/streptomycin (GIBCO, Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard chromatin extraction procedures were utilized for ChIP analysis using anti-Beaf32 or anti-IgG control antibodies
ChIP samples were prepared for sequencing using standard Illumina protocols of ChIP sample prep kits from 12 ng of starting precipitated DNA to generate sequencing libraries
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP-Seq with anti-RNAPII antibodies (Covance)
|
| Data processing |
S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/ (GIBCO, Invitrogen).
S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 or luc were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.
Chromatin was sonicated (Bioruptor) followed by immunoprecipitations with anti-H3K36-me2 or me3 specific antibodies or anti- RNA Polymerase II specific antibodies
Illumina library preparation by TruSeq.
ChIP-Seq
Genome_build: Flybase release 5.41
Supplementary_files_format_and_content: tab-delimited text files
|
| |
|
| Submission date |
Apr 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Olivier Cuvier |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
LBME
|
| Lab |
Chromatin Dynamics & Cell proliferation
|
| Street address |
118 route de Narbonne
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE57165 |
Illumina Sequencing data of Insulator Proteins and the co-factor dMes-4 |
| GSE57168 |
Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes |
|
| Relations |
| BioSample |
SAMN02740909 |
| SRA |
SRX529168 |
