|
| Status |
Public on Aug 13, 2009 |
| Title |
Pupae_H3K9Me3_ChIPSeq_1 |
| Sample type |
SRA |
| |
|
| Source name |
Pupae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
development point: Pupae
antibody: H3K9me3
antibody manufacturer: Abcam
antibody catalog number: ab8898
antibody lot number: 422485
|
| 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 pupae at 1-2 days APF (after puparium formation), 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. Pupae are collected 2 days after the first pupa formed on the wall of the bottle. They are collected with a brush humidified with EWB and placed into an eppendorf tube. They are rinsed extensively with EWB and cross-linked 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 |
corresponding input record: GSM400665
|
| 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 300Â 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 |
Aug 12, 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 (3) |
| 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 |
| GSE18572 |
Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila |
|
| Relations |
| SRA |
SRX013095 |
| BioSample |
SAMN00005244 |
| Named Annotation |
GSM439449_Pupae_H3K9Me3.merged.bed.wig.final.bed.trim.bed.significant.bed.gz |
