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Sample GSM511087 Query DataSets for GSM511087
Status Public on Feb 18, 2010
Title Dmel-CAD_ChIP-Seq
Sample type SRA
 
Source name blastoderm embryos
Organism Drosophila melanogaster
Characteristics strain: Oregon R
developmental stage: blastoderm embryo
developmental time: 2 - 3 hrs
fragment (size-selected): 250 bp
antibody: CAD
Growth protocol Embryos collected from large population cages for 1 hour, aged to appropriate stage, fixed in formaldehyde, chromatin isolated by CsCl gradient ultracentrifugation, fragmented and immunoprecipitated with affnity-purified antibody
Extracted molecule genomic DNA
Extraction protocol DNA fragments were converted to phosphorylated blunt ends using T4 DNA polymerase, Klenow DNA polymerase, and T4 polymerase kinase, a 3' A base overhang was added using Klenow DNA polymerase exo- (3' to 5' exo minus), and Illumina adapters were ligated to the fragments. We carried out the PCR step for enrichment of adapter-modified DNA prior to the library size selection, and limited the amplification to 10-13 cycles to minimize the potential bias associated with PCR amplification. After the amplification step, we size-selected DNA fragments of 150-500 bp (including the adapter sequence) for BCD, HB, GT, and KNI samples, and 200 - 500 bp for KR and CAD.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description chromatin IP against CAD
Data processing We used the Apr. 2006 assembly (dm3, BDGP Release 5) of the D. melanogaster genome, downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/chromFa.tar.gz and the Nov. 2005 assembly (droYak2) of the D. yakuba genome, downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/droYak2/bigZips/chromFa.tar.gz. We trimmed all sequenced tags to 20 bp and mapped the tags to the genomes using Bowtie v0.9.9.1 [22] with command-line options ‘-v 1 -m 1’, thereby keeping only tags which mapped uniquely to the genome with at most one mismatch. We called peaks for each experiment using MACS v1.3.5 [25] with the option ‘--pvalue 0.00001’. We used total chromatin as background controls, and set the ‘--mfold’ option to the maximum value for which MACS could find a sufficient number of paired peaks. In order to only consider peaks for which we could reliably assign orthology and to control for potential assembly errors in the draft D. yakuba genome, we used exonerate [35] to search for peaks whose associated sequence was duplicated in either genome. For each peak, we 1) searched for duplicated sequence in the genome where the peak was called, and 2) used the whole-genome alignment to pull out the orthologous sequence in the other genome and searched for duplicates of that sequence in the other genome, which frequently indicated a potential assembly error due to the unfinished nature of the D. yakuba assembly. We discarded any peaks whose associated sequence was duplicated in either genome.
 
Submission date Feb 17, 2010
Last update date Jun 11, 2013
Contact name Michael Eisen
E-mail(s) mbeisen@berkeley.edu
Phone 510-666-3639
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Eisen Lab
Street address Stanley Hall 304B
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL9061
Series (1)
GSE20369 Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species
Relations
BioSample SAMN02196421

Supplementary file Size Download File type/resource
GSM511087_Dmel-CAD.bwtout.txt.gz 78.9 Mb (ftp)(http) TXT
GSM511087_Dmel-CAD.peaks.gff.gz 93.5 Kb (ftp)(http) GFF
Processed data provided as supplementary file

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