NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM694131 Query DataSets for GSM694131
Status Public on Mar 23, 2011
Title 0-24h Embryo PolII ChIP-Seq extraction4_seq1 aliquote 1
Sample type SRA
 
Source name 0-24h Embryo PolII ChIP-Seq extraction4_seq1 channel_1
Organism Drosophila melanogaster
Characteristics developmental stage: Mixed Embryos 0-24h
Growth protocol Embryo collection protocol
Extracted molecule genomic DNA
Extraction protocol Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol. This includes a 150-200bp size selection step.
Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description channel ch1 is input DNA;
Data processing Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database. Processed data are obtained using following parameters: genome version is 5.1 ChIPseq_analysis:DM:1 protocol. * WIG Track Generation: o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function. o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function. o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics. o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates. * GFF3 Peak Call Generation: o MAQ files were converted to ELAND using an in-house script. o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script. o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05. o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.
 
Submission date Mar 21, 2011
Last update date May 15, 2019
Contact name DCC modENCODE
E-mail(s) help@modencode.org
Phone 416-673-8579
Organization name Ontario Institute for Cancer Research
Lab modENCODE DCC
Street address MaRS Centre, South Tower, 101 College Street, Suite 800
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platform ID GPL9058
Series (1)
GSE28068 24 Hour RNA PolII ChIP-Seq experiment
Relations
SRA SRX050605
BioSample SAMN00253861

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.