|
| Status |
Public on Oct 30, 2015 |
| Title |
Hnf4_ChIPSeq_1 and 2 |
| Sample type |
SRA |
| |
|
| Source name |
E16-24
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: E16-24
antibody name: Hnf4
manufacturer: White Lab
lot/batch#: N/A
catalog: N/A
strain: ISO1
|
| 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 |
After chromatin immuno-precipitation, the DNA is purified in 30ul of water. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| 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 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.
|
| |
|
| Submission date |
Dec 21, 2011 |
| Last update date |
Nov 20, 2015 |
| 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) |
| GSE23537 |
modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data |
| GSE34610 |
modENCODE_White Lab: genome-wide ChIP data of Hnf4 from E16-24 on Illumina Genome Analyzer. |
|
| Relations |
| BioSample |
SAMN00768999 |
