|
| Status |
Public on Aug 11, 2010 |
| Title |
10T-E16-24h_GFP_INPUT_1 |
| Sample type |
SRA |
| |
|
| Source name |
10T-E16-24h
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 10T-E16-24h
fraction: input
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. y w, VK37 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 material is crushed in a glass homogenizer in presence of 1.8% of formaldehyde for 15 minutes at room temperature. 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 Input reference sample. 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. If used for hybridization on microarrays, the sample will undergo an LM-PCR amplification before labelling.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Reads were aligned to the flybase BDGPv5 reference genome using Bowtie. Signal files were generated with the R package SPP. Peaks were called with MACS.
|
| |
|
| Submission date |
Jul 23, 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 (2) |
| GSE23126 |
modENCODE_White Lab: genome-wide ChIP data of GFP from 10T-E16-24h on Illumina Genome Analyzer. |
| GSE23537 |
modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data |
|
| Relations |
| SRA |
SRX025471 |
| BioSample |
SAMN00100794 |
