|
| Status |
Public on Nov 10, 2014 |
| Title |
OrR_gamma-H2Av |
| Sample type |
SRA |
| |
|
| Source name |
third instar salivary gland from OrR
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: OrR
chip antibody: gamma-H2Av (Rockland)
developmental stage: third instar
tissue: salivary gland
|
| Treatment protocol |
Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium and frozen within less than 30 min in liquid nitrogen. When enough were collected, ChIP was performed with either anti gamma-H2Av antibody (Rockland) or rabbit IgG (Abcam)
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Salivary glands were dounced and sonicated using a Biorupto 300 (Diagenode)
Libraries were constrcted using the NEB Next ChIP seq kit (Part # E6200S) according to manufactures recommendations with indexing primers for multiplexing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
OrR 3SG gamma-H2Av ChIP
|
| Data processing |
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to the dm3 genome assembly using BWA using the default parameters with the exception of no gaps allowed (-o 0)
Data were filtered using the following specifications…
Peaks were called using MACS v1.4 with the following setting; -tsize=40 --wig --space=25 --mfold=10,30 --pvalue=1e-5. Peaks were further filtered based on the FDR. Peaks with a FDR of <5% were included in the analysis
Genome_build: dm3
Supplementary_files_format_and_content: MACS peak files. Information include: chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region (e.g. pvalue =1e-10, then this value should be 100), fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage. Coordinates in .txt is 1-based which is different with BED format.
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Terry L. Orr-Weaver |
| E-mail(s) |
weaver@wi.mit.edu
|
| Phone |
617-258-5251
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Orr-Weaver
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE55932 |
ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila; ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers |
| GSE56056 |
SuUR role in regulation of DNA replication |
|
| Relations |
| BioSample |
SAMN02689379 |
| SRA |
SRX490730 |
