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Sample GSM594216 Query DataSets for GSM594216
Status Public on Sep 16, 2010
Title NW-GFP-Goat[Dfd]_ChIPSeq_1 and 2
Sample type SRA
 
Source name E0-8h
Organism Drosophila melanogaster
Characteristics developmental stage: E0-8h
antibody name: NW-GFP-Goat[Dfd]
antibody manufacturer: White Lab
lot/batch#: N/A
catalog: Custom
Treatment protocol No Treatment
Growth protocol 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 version 0.12.5. Signal files were generated with the R package version 2.7.1 SPP 1.0. Peaks were called with MACS version 1.3.7.
 
Submission date Sep 15, 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)
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
GSE24137 modENCODE_White Lab: genome-wide ChIP data of NW-GFP-Goat[Dfd] from E0-8h on Illumina Genome Analyzer.
Relations
SRA SRX026861
BioSample SAMN00113382
Named Annotation GSM594216_E0-8h_10T_Dfd_-GFP_peaks.bed.gz

Supplementary file Size Download File type/resource
GSM594216_E0-8h_10T_Dfd_-GFP_density.bedgraph.gz 21.4 Mb (ftp)(http) BEDGRAPH
GSM594216_E0-8h_10T_Dfd_-GFP_peaks.bed.gz 9.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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