|
| Status |
Public on Aug 11, 2010 |
| Title |
hkb_ChIPSeq_1 and 2 |
| Sample type |
SRA |
| |
|
| Source name |
E8-16h
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: E8-16h
fraction: ChIP
antibody name: KW3-hkb-D1
manufacturer: White Lab/Aviva
lot/batch#: N/A
catalog#: N/A
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.
|
| 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) |
| GSE23123 |
modENCODE_White Lab: genome-wide ChIP data of hkb from E8-16h on Illumina Genome Analyzer. |
| GSE23537 |
modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data |
|
| Relations |
| SRA |
SRX025464 |
| BioSample |
SAMN00100788 |
| Named Annotation |
GSM569793_E8-16h_hkb_peaks.bed.gz |
