|
| Status |
Public on Apr 16, 2010 |
| Title |
S2 H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2, ATCC, CLR-1963, Lot#5054622
antibody: H3K4me3
antibody manufacturer: Abcam
antibody catalog number: ab8580
|
| Growth protocol |
The Drosophila S2 cells were cultured following the manufacturer’s protocol. Exponentially growing S2 cells were harvested and resuspended in digestion buffer (50mM Tris-HCl, pH7.6, 1mM CCl2, 0.2% Triton X-100, 5mM butyrate, 1x proteinase inhibitor cocktail and 0.5mM PMSF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from approximately 2x10^7 cells were used for each ChIP experiment. End repair for ChIP fragments was performed using PNK and Klenow enzyme, followed by treatment with Taq polymerase. Sequencing adaptors were ligated to the repaired ends and ChIP DNA was amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against H3K4me3
|
| Data processing |
The 25-bp sequencing reads were obtained from the Illumina Genome Analyzer (GA) Pipeline. All reads were aligned to the Drosophila genome (dm3) using the ELAND (Efficient Local Alignment of Nucleotide Data) software, allowing up to two mismatches with the reference sequence. Only uniquely mapped reads were retained. For multiple identical reads, at most three copies were retained to reduce the possibility of biases from PCR amplification. The output of the GA Pipeline was converted to browser extensible data (BED) files. The bedgraph files used for visualization on the UCSC browser were generated from the uniquely mapped reads using a 4-bp window as previously described ( Barski A, et al. Cell 2007).
|
| |
|
| Submission date |
Dec 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
dschones@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (1) |
| GSE19325 |
Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis |
|
| Relations |
| SRA |
SRX017849 |
| BioSample |
SAMN00010224 |
| Named Annotation |
GSM480156_dm3-S2-H3K4me3.bed.gz |
