|
| Status |
Public on May 12, 2009 |
| Title |
AdultFemale_INPUT |
| Sample type |
SRA |
| |
|
| Source name |
AdultFemale
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: AdultFemale
reference: input
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. y; bw cn sp flies are cultivated in cages with apple juice agar plates covered with yeast powder. 2. For a collection of Drosophila Adult Female 2-3 days old, new plates are added after a 2 hours pre-egglaying at 9 am and flies are allowed to lay eggs for 24 hours. Embryos covered plates are then cut and placed back into regular fly medium bottles. 3. Adult flies are collected 2 to 3 days after the first adult hatched. They are sorted for sex under a dissecting microscope after being put to sleep with CO2. Females and males are placed into different eppendorff tubes on ice and then rinsed with EWB before cross-linking in 1.8% formaldehyde at room temperature for 15 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Drosophila samples are crushed in presence of 1.8% of formaldehyde for 15 minutes. 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 |
AdultFemale_INPUT
|
| Data processing |
Reads were aligned to the flybase BDGPv5 reference genome, and the fragment count at any given position (10-bp resolution) was estimated as the number of uniquely aligned reads oriented towards it and within 300 bp. Enriched intervals were identified by comparison of the mean fragment count in 1-kb windows against a sample-specific expected distribution estimated by randomization (H3K4me3, H3K27me3), or using a supervised Hidden Markov Model (H3K36me3, H3K9me3, H4K20me3).
|
| |
|
| Submission date |
May 07, 2009 |
| 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) |
| GSE15292 |
Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq |
| GSE16013 |
Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq |
|
| Relations |
| SRA |
SRX013018 |
| BioSample |
SAMN00005167 |
