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Sample GSM602335 Query DataSets for GSM602335
Status Public on Nov 08, 2012
Title Dpse_WPP_CTCF_ChIPSeq_1, 2 and 3
Sample type SRA
 
Source name white prepupae
Organism Drosophila pseudoobscura
Characteristics developmental stage: white prepupae
antibody name: CTCF-C
antibody manufacturer: Renkawitz Lab
antibody lot/batch#: N/A
antibody catalog: Custom
fraction: ChIP
Treatment protocol No Treatment
Growth protocol The four sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval
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 Alignment: Sequence reads were obtained and mapped to multiple drosophila genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the QuEST 2.0 algorithm (http://mendel.stanford.edu/SidowLab/downloads/quest/)
 
Submission date Sep 30, 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 GPL9395
Series (1)
GSE24449 Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer
Relations
SRA SRX027397
BioSample SAMN00113739

Supplementary file Size Download File type/resource
GSM602335_dpse_combined_signal_wpp_CTCF_QuEST_CDP_scores.wig.gz 325.5 Mb (ftp)(http) WIG
GSM602335_dpse_peak_region.bed.gz 19.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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