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Sample GSM1015344 Query DataSets for GSM1015344
Status Public on Oct 04, 2012
Title KC167 WT Mid-Late S-phase Replicate 1 extraction3_seq1 aliquote 1
Sample type SRA
 
Source name KC_WT_MidLateSphase_1
Organism Drosophila melanogaster
Characteristics cell line: Kc167
tissue: embryo-derived cell-line
developmental stage: late embryonic stage
genotype: se/e
Sex: Female
Growth protocol The general growth protocol for growing Drosophila cell lines in culture.
Extracted molecule genomic DNA
Extraction protocol DNA isolation from Drosophila cell lines. RNAse-treated cellular extract is treated with ethanol in order to precipitate DNA.
Cells are pulse labeled with 50ug/ml BrdU for one hour, and washed with 1x PBS.
FACS Protocol.1. Spin cells down and resuspend in 300µl of PBS. (For large pellets increase this volume and increase the EtOH volume proportionally)2. Fix by adding 5ml of 70% EtOH Dropwise while vortexing gently, incubate at -20ºc for at least 30 minutes.3. Spin, remove EtOH and resuspend in 5ml PBS. Allow cells to rehydrate at 4ºc for at least an hour.4. Spin and resuspend the cells in 4ml of PBS with 10µg/ml RNaseA and 10µg/ml PI. Incubate at RT for at least 30min up to several hours (alternatively incubate for 10min at 37ºc)Cells were sorted into early mid and late S-phase fractions using a FACS Vantage SE (BD Biosciences) equipped with the DiVa acquisition system.
An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA.
Generation of a genomic library suitable for Illumina sequencing.Generation of a genomic library suitable for Illumina sequencing. The procedure starts with random shearing of genomic DNA with sonication followed by Illumina-developed sample preparation protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Illumina_sequencing:DM:1 protocol. Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina HiSeq 2000 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). Processed data are obtained using following parameters: read length is 50 Bowtie alignment:DM:1 protocol. For paired end CNV:Using the default setting, Bowtie2 was used to align paired sequenced reads to the reference genome. Single end HiSeq RepliSeq:Bowtie was used to align sequenced reads to the reference genome, with the following parameters:--phred33-quals -p 6 -n 2 -l 20 -m 1 -k 1 -S -y --best --strata Processed data are obtained using following parameters: genome version is 5.1 Illumina sequencing WIG Generation RPKM from BAM:DM:1 protocol. For Repliseq experiments, a bin size of 10000 bp stepping every 2500 bp was used.
 
Submission date Oct 04, 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 GPL13304
Series (1)
GSE41349 KC WT Repliseq
Relations
SRA SRX193628
BioSample SAMN01761661
Named Annotation GSM1015344_dm198.wig.gz

Supplementary file Size Download File type/resource
GSM1015344_dm198.wig.gz 120.6 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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