|
| Status |
Public on Aug 01, 2013 |
| Title |
GAF-KD GAF ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells depleted of GAF by RNAi
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ModENCODE S2-DRSC (lot 181A1)
antibody: anti-GAF
|
| Growth protocol |
S2-DRSC (lot 181A1) cells were grown in Schneider’s media (Sigma) with 10% FBS (lot ASD29137).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP protocol has been previously described (PMID: 20844575). In short, S2-DRSC (lot 181A1) cells were grown in Schneider's media with 10% FBS (lot ASD29137) and crosslinked with a final concentration of 2% paraformaldhyde for one minute. Crosslinking was quenched by the addition of glycine to a final concentration of 250 mM and the extract was sonicated as previously described (PMID: 20844575). The Protein-A beads were blocked with BSA (1 mg/ml) and Polyvinylpyrrolidone (1 mg/ml) prior to the IP and freshly thawed antiserum was used for each IP.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNAi treated with GAF dsRNA (10ug/ml) for five days.
|
| Data processing |
alignment with bwa. Parameters: bwa aln -n 4 dm3.fasta GAF_ChIP_combined.txt.gz > GAF_ChIP_combined.sai
alignment with bwa. Parameters: bwa aln -n 4 dm3.fasta GAF_RNAi_GAF_ChIP_combined.txt.gz > GAF_RNAi_GAF_ChIP_rep1.sai
peak calling macs14 version 1.4.0. Parameters: macs14 -t GAF_chip_gafKD_reps.unique.sam -c combined_PREimmune.unique.sam --name=GAF_chip_mockKD_reps --gsize=165000000 --tsize=46 --mfold=10,10000 --bw=150 --wig --pvalue=0.0001 --call-subpeaks
peak calling macs14 version 1.4.0. Parameters: macs14 -t GAF_chip_mock_reps.unique.sam -c combined_PREimmune.unique.sam --name=GAF_chip_mockKD_reps --gsize=165000000 --tsize=46 --mfold=10,10000 --bw=150 --wig --pvalue=0.0001 --call-subpeaks
Genome_build: dm3
Supplementary_files_format_and_content: Processed files are linked to GSE40646 and include the wiggle, bed, peaks, subpeaks, and summit files from peak calling. File GSE40646_readme.txt details derivation of each processed file. Pre-immune ChIP was submitted previously to GEO as GSM470838.
|
| |
|
| Submission date |
Sep 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Joseph Guertin |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Connecticut
|
| Department |
Center for Cell Analysis and Modeling
|
| Lab |
Molecular Genomics
|
| Street address |
400 Farmington Ave
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE40646 |
The Genomic Binding Profile of GAGA Element Associated Factor (GAF) in Drosophila S2 cells |
|
| Relations |
| SRA |
SRX183521 |
| BioSample |
SAMN01162332 |
