|
| Status |
Public on Nov 10, 2014 |
| Title |
OrR_st10_IgG |
| Sample type |
SRA |
| |
|
| Source name |
stage 10 egg chambers from OrR
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: OrR
chip antibody: IgG (made in-house)
developmental stage: stage 10
tissue: egg chamber
|
| Treatment protocol |
Ovaries were dissected into EBR mediumand fixed in 2% formaldehyde. Ovaries were resuspended in LB3 and indiviudal egg chambers were isolated. When enough were collected (600 per ChIP reaction), ChIP was performed with either anti-SUUR, anti-Cdc45 or GP IgG
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.Females were fattend for two days on wet yeast
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Egg chambers 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 stage 10 IgG 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 MACS2 default settings and a p value of 10-3.
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 |
Sep 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Terry L. Orr-Weaver |
| E-mail(s) |
[email protected]
|
| 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 |
SAMN03074566 |
| SRA |
SRX706812 |
