|
| Status |
Public on Jan 26, 2010 |
| Title |
21d-Female-7T(cad-GFP)-ChIPSeq_1 |
| Sample type |
SRA |
| |
|
| Source name |
A-Female_7T_ChIPSeq_1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
development stage: Adult-Female
antibody: goat anti GFP
test: ChIP
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. y w, VK33 flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a 0-4 hours egg laying for example, new plates are added after a 2hours pre-egglaying and flies are allowed to lay eggs for 4 hours. 3. Embryos are collected using a filter mesh and a brush. They are rinsed with EWB and cross-linked in 1.8% formaldehyde at room temperature for 15 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila whole animals (embryos, larvae, pupae or adults) are crushed in presence of 1.8% of formaldehyde for 15 minutes with the help of a douncer. After washing, the material is sonicated for 15 minutes to solubilize the chromatin. After centrifugation, the supernatant containing soluble chromatin is collected for IPs. Specific antibodies are added to the chromatin extract while one aliquot will be treated for DNA extraction corresponding to the reference samples. ChIP are carried overnight at room temperature. Protein A Sepharose beads are used to pull down the chromatin bound antibodies. After washes and finally elution, the DNA corresponding to the IPed material is extracted and purified. The DNA is directly used for Solexa library preparation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
A-Female_7T_ChIPSeq_1
corresponding input record(s): GSM499632
|
| Data processing |
Reads were aligned to the flybase BDGPv5 reference genome using the Illumina Genome Analyzer Pipeline Software. Signal files were generated with the R package SPP. Peaks were called with MACS (parameters: --format=ELAND --gsize=120000000 --tsize=36 --bw=250 --mfold=2 --pvalue=1e-3).
|
| |
|
| Submission date |
Jan 22, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL9058 |
| Series (1) |
| GSE20000 |
Genome-wide maps of chromatin state in staged Drosophila embryos and cell lines. |
|
| Relations |
| SRA |
SRX016140 |
| BioSample |
SAMN00008253 |
| Named Annotation |
GSM499631_A-Female_7T_peaks.bed.gz |
