|
| Status |
Public on Aug 31, 2017 |
| Title |
S2_Rpb3_ChIPSeq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
S2 Cell line
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: late embryo-derived cell line
strain: S2-DRSC
genotype: wild type
treatment: 10 microMolar Cu2SO4
chip antibody: Rpb3 (a gift from Dr. K Adelman - Gilchrist et al., (2010) Cell 143(4):540-551)
input dna code: B
|
| Treatment protocol |
Cells were treated with 10 microMolar Copper Sulphate for 24 h prior to chromatin and RNA preparation
|
| Growth protocol |
Cells were grown in T-flasks to a density of not more than 7x10^6 cells/ml in Schneider Medium supplemented with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared according to the modENCODE procedure; RNA was extracted with Qiagen Rneasy kit
DNA libraries were prepared according to Illumina's instructions; RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Rpb3 ChIP-Seq of S2 cells Rep2
S2_Rpb3_ChIP_peaks.bed
S2_Rpb3_ChIP.bigWig
|
| Data processing |
Basecalls performed using RTA (Illumina)
ChIP-seq reads were aligned to the dm3 genome assembly using BWA v0.7.12 using default parameters
ChIP-Seq peak calling was performed using MACS2 (v0.7.12) using low stringency on individual replicates. Final peaks were called using an Irreproducible Discovery Rate (IDR) of 1% according to guidelines set out by the ENCODE consortium.
ChIP-seq bigWig files of enrichment >0 were produced using spp using merged replicate bamfiles that had been randomly downsampled to have equal numbers of reads between samples from S2 cells and those from S2-HA::AbdA cell line
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files were prepared using spp and show ChIP enrichment values >0; Bed files were prepared using MACS2 and represent peaks called in both replicates having an IDR of 1%.
|
| |
|
| Submission date |
Jul 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Saurin |
| E-mail(s) |
[email protected]
|
| Organization name |
IBDM / CNRS
|
| Street address |
Campus de Luminy
|
| City |
Marseille |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE101554 |
Genomic binding profiling upon expression of AbdA in S2 cells |
| GSE101557 |
Expression of Hox transcription factors in Drosophila S2 cells |
|
| Relations |
| BioSample |
SAMN07360980 |
| SRA |
SRX3011230 |
