|
| Status |
Public on Jun 18, 2015 |
| Title |
OrR_stage10B_gammaH2Av_ChIP_1 |
| Sample type |
SRA |
| |
|
| Source name |
OrR stage 10B follicle cell nuclei
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain background: OregonR
genotype/variation: wild type
developmental stage: 10B
tissue: egg chamber
chip antibody: Anti-Histone H2AvD pS137 (RABBIT) Antibody
chip antibody vendor: Rockland Immunochemicals
chip antibody cat.#: 600-401-914S
chip antibody lot#: 27144
|
| Treatment protocol |
Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Ovaries were teased apart and fixed in 4% formaldehyde. Ovaries were resuspended in PBS and stage 10B and 13 egg chambers were isolated. Fixed egg chambers were stored at -80ᵒC until 3,000 egg chambers from each genotype were collected. Follicle cell nuclei were isolated from egg chambers prior to ChIP with anti-gammaH2Av (Rockland).
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Egg chambers were dounced and sonicated using a Bioruptor 300 (Diagenode).
Libraries were constructed 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 follicle cell stage10B gammaH2Av ChIP
processed data file: WTst10B_ChIP_SW_log2_Aver.txt
WT_10B_gammaH2Av_ChIP_1
|
| Data processing |
Reads were mapped with bowtie setting the seed length to 40, using the option “--best”, and leaving other settings as default.
One kilobase windows were made sliding every 100 nucleotides, and the number of reads overlapping with the windows were counted using “bedtools coverage”
The number of reads in each window was divided by the millions of reads mapped to obtain reads per million (RPM).
The RPM from the ChIP was divided by the RPM of the corresponding i nput in each window. To avoid divisions by zero 10-6 was added to each RPM value before taking the ratio.
The two replicates were summarized by calculating the mean of the log2ratios (ChIP/input).
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: text file with four columns: chr, sliding window start, sliding window start stop, mean of the log2ratios (ChIP/input) of the 2 replicas.
|
| |
|
| Submission date |
Mar 09, 2015 |
| 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) |
| GSE66689 |
gammaH2Av ChIP-seq in Drosophila stage 10B and 13 follicle cells |
| GSE66691 |
Replication fork progression during re-replication requires the DNA damage checkpoint and double-strand break repair |
|
| Relations |
| BioSample |
SAMN03395020 |
| SRA |
SRX914952 |
