|
| Status |
Public on Mar 13, 2020 |
| Title |
Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_rep2_Input |
| Sample type |
SRA |
| |
|
| Source name |
Dm_S2cell_dBRD4_ChIPseq_GST_RNAi_Input
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line background: S2 cells
genotype/variation: wild type
knockdown or inhibitor treatment: control RNAi (GST)
chip antibody: dBRD4 antibody reconizing short and long isoform ID166 (Paro lab)
|
| Treatment protocol |
for RNAi: dsRNA was added to the cell culture medium, 10µg dsRNA per 1mio cells, cells were harvested after 4 days of RNAi, for dBRD4 inhibitor treatments: DMSO or inhibitor was added to the cell culture medium
|
| Growth protocol |
Drosophila S2 cells (Invitrogen) were cultured in Express Five SFM media (Thermo Fisher) supplemented with 10% (v/v) Glutamax (Thermo Fisher). Cultures were maintained adherent or in shaking incubators at 27ºC at a speed of 80
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
cells were fixed for 10min in 1.8% of formaldehyde at 23 °C, nuclei were isolated, chromatin was fragmented by sonication (Covaris), The lysate was clarified by centrifugation before immunoprecipitation, and eluted by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using AMPure XP Beads (Beckman Coulter); for Rpb3 ChIP experiments Drosophila Virilis chromatin was added prior to IP as spike control. For Biotin ChIP experiments exogenous Biotin-labeled DNA fragments were added prior to IP as spike control.
NEB Next Ultra II
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
dBRD4=fs(1)h , dBRD4-S indicating short isoform of dBRD4
|
| Data processing |
Paired-end 75 bp reads were trimmed (TrimGalore, quality threshhold 20), then mapped using Bowtie2, BAM files of biological replicates were merged using SAM Tools
Coverage files were generated with deepTools3 (v3.0.1) bamCompare with a binsize of 1 (bin size of 10 for H3 profiles). The X chromosome was ignored for scaling. The data was normalized as follows: log2FC over Input for Drosophila H4K16ac, H3, Rpb3; Input subtraction for Drosophila Biotin-dBRD4-S and dBRD4. For Rpb3 profiles SES scaling (signal extraction method) was applied
Genome_build: dm6
Supplementary_files_format_and_content: bigwig file format, Input normalized ChIP enrichments
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Mar 13, 2020 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23323 |
| Series (2) |
| GSE135771 |
Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation |
| GSE135815 |
Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation |
|
| Relations |
| BioSample |
SAMN12566549 |
| SRA |
SRX6708261 |
