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Sample GSM881216 Query DataSets for GSM881216
Status Public on Feb 27, 2012
Title 4-7hr ORC ChIP-Seq Input Oregon-R strain
Sample type SRA
 
Source name 4-7hr ORC ChIP-Seq Input Oregon-R strain
Organism Drosophila melanogaster
Characteristics strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type )
developmental stage: Embryo 4-7h
genotype: wild type
Growth protocol Using newly eclosed females fattened on wet yeast paste, collect embryos for up to four hours on apple juice plates. To ensure that females have not been holding embryos, precollect embryos for one hour. Wash embryos off the four-hour collection dish with PBS; dechorionate in 50% bleach for 3 minutes, and collect dechorionated embryos with a fine nylon mesh screen.
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 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 WIG Generation:DM:1 protocol. WIG Track Generation: * Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function. * Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function. * 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. * To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.
 
Submission date Feb 27, 2012
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)
GSE36106 4-7 Hour ORC ChIP-Seq experiment
Relations
SRA SRX124474
BioSample SAMN00793076

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

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