|
| Status |
Public on Apr 04, 2015 |
| Title |
GAF-RNAi replicate 3 (H2AvD MNase-ChIP) |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell line
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cells
treatment: GAF-RNAi
chip antibody: Anti-H2AvD antisera (Glaser lab stock)
|
| Treatment protocol |
cells treated with double-stranded RNA against Beta-galactosidase (LacZ-RNAi control) or GAGA factor for 5 days
|
| Growth protocol |
Cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ten million cross-linked nuclei were digested with MNase until about 80% of the material has mononucleosome-sized. For H2AvD nucleosomes, immunoprecipitated with 4ul Anti-H2AvD antisera (Glaser lab stock) from 75ul of digested material. Cross-links were reversed at 65°C and the DNA was extracted with phenol:chloroform and precipitated. 50ng of non-immunoprecipitated (MNase-seq) or immunoprecipitated (H2AvD) DNA was ligated to Tru-seq paired-end adapters. The resulting DNA was PCR amplified for 5 cycles and 200-400bp fragments were selected and PCR amplified for 12-15 cycles. The cDNA was then paired-end sequencing was performed (50 bases) on the Illumina HiSeq 2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MNase digested chromatin
H2AvD immunoprecipitated MNase digested cross-linked chromatin from GAF-RNAi S2 cells
|
| Data processing |
Library strategy: MNase-ChIP-Seq
paired-end sequencing separated into individual libraries by bar-codes
reads filtered based sequencing quality filter
paired reads mapped using bowtie2 (--no-mixed --no-discordant)
reads 120-180bp selected
Genome_build: Release 5 (dm3)
Supplementary_files_format_and_content: bedgraph file of the complete paired-end reads
|
| |
|
| Submission date |
Jul 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Fuda |
| E-mail(s) |
njf6@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Street address |
417 Biotechnology Building, Cornell University
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE58956 |
GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing [MNase] |
| GSE58957 |
GAGA Factor maintains promoters in nucleosome-free conformation and allows promoter-proximal pausing |
|
| Relations |
| BioSample |
SAMN02898409 |
| SRA |
SRX643415 |
