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Sample GSM1230341 Query DataSets for GSM1230341
Status Public on Sep 13, 2013
Title D. yakuba ChIP-seq rep 1
Sample type SRA
Source name Dyak_WPP
Organism Drosophila yakuba
Characteristics developmental stage: White prepupa
chip antibody: H3K27me3
Growth protocol 1. the iso1 (y; bw cn sp) 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.
ChIP and input libraries were prepared for sequencing using standard Illumina 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.
Genome_build: droYak2 (D. yakuba)
Submission date Sep 12, 2013
Last update date May 15, 2019
Contact name Kevin P. White
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 GPL11000
Series (2)
GSE23537 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-Seq data
GSE50819 modENCODE_White Lab: genome-wide ChIP-chip and ChIP-seq data [D. yakuba H3K27me3]
BioSample SAMN02356000
SRA SRX349452
Named Annotation GSM1230341_dyak_WPP_R1.wig.gz

Supplementary file Size Download File type/resource
GSM1230341_dyak_WPP_R1.wig.gz 22.4 Mb (ftp)(http) WIG
GSM1230341_dyak_WPP_R1_peaks.bed.gz 162.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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