|
| Status |
Public on Jun 30, 2013 |
| Title |
DmS2DRSC_ChIP_FSH_ID166 |
| Sample type |
SRA |
| |
|
| Source name |
DRSC-S2 cell line
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: DRSC-S2 cell line
chip antibody: FSH_ID166 [raised against the N-terminal, common part of FSH-S and FSH-L, protein 1.2]
chip antibody supplier: gift from Igor Dawid
|
| Growth protocol |
Drosophila S2-DRSC cells were grown in Schneiderâs Drosophila Medium (Invitrogen) supplemented with 10 % FBS (Hyclone) at 25°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin fixation and immunoprecipitation were performed essentially as described in (Orlando V et al. (1997) Methods 11:205â214.). Cells (1x109) were fixed in 200-ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 200â400 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. Polyclonal rabbit antibodies for two different epitopes in Ash1 were a gift from Frank Sauer, Riverside. Polyclonal rabbit antibodies for FSH were a gift from Igor Dawid. The antibody ID173 was raised against protein 4.1 (recognizes FSH-L only) and ID166 was raised against the N-terminal, common part of FSH-S and FSH-L, protein 1.2. The cDNAs used for the expression of both antigenes have been described in (Haynes et al. (1989) Dev.Biol. 134) Libraries for sequencing were prepared with the ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 (ChIP-seq) cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
ChIP-seq reads were quality filtered (FASTX Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html), fastq_quality_filter, parameters -Q 33-q 30 -p 75) and subsequently aligned with bowtie (default parameters) (Langmead2009) to the Flybase Drosophila melanogaster reference genome r5.22. For alignment file manipulation, Samtools were used LiSamtools2009.
|
| |
|
| Submission date |
Jul 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Beisel |
| E-mail(s) |
christian.beisel@bsse.ethz.ch
|
| Phone |
+41 61 387 31 65
|
| Organization name |
ETH Zurich
|
| Department |
Biosystems Science and Engineering
|
| Lab |
Genomics Facility Basel
|
| Street address |
Mattenstrasse 26
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE30820 |
Chromatin maps of the Drosophila melanogaster TrxG protein Ash1 and FSH |
|
| Relations |
| SRA |
SRX084581 |
| BioSample |
SAMN00672586 |
