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Sample GSM1900399 Query DataSets for GSM1900399
Status Public on Oct 08, 2015
Title control_RNAi_rep2
Sample type SRA
 
Source name Kc167
Organism Drosophila melanogaster
Characteristics experiment: early origin
chip antibody: Mouse anti-BrdU (BD Biosciences #555627)
RNAi treatment: control
Growth protocol Drosophila Kc167 cells were cultured at 25℃ in Schneider’s Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Gemini) and 1% penicillin/streptomycin/glutamine (Invitrogen).
Extracted molecule genomic DNA
Extraction protocol In early origin experiments, chromatin was isolated and BrdU was immunoprecipted as described in (Ryba et al., Nat Protoc, 2011). H4K20me1 and γ-H2Av ChIP were performed as described in (MacAlpine et al., Genome Research, 2010).
Sequencing libraries were prepared using Illumina's TruSeq protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 30 -m 1 --best --strata -y.
RPKM (reads per thousand kb, per million mappable reads) was determined with RSamtools and GenomicRanges packages in R. For early origin and H4K20me1 experiments, genome is divided into 10 kb bins stepping every 1 kb. For γ-H2Av experiment, genome is divided into nonoverlapping 5 kb bins.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: csv files with columns chr, start,end,RPKM.
 
Submission date Oct 01, 2015
Last update date May 15, 2019
Contact name Jason Alan Belsky
E-mail(s) jason.belsky@duke.edu
Organization name Duke University
Department Pharmacology and Cancer Biology
Lab David MacAlpine Lab
Street address LSRC Room C333
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL16479
Series (1)
GSE73668 Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila
Relations
BioSample SAMN04126433
SRA SRX1299927

Supplementary file Size Download File type/resource
GSM1900399_control_RNAi_rep2_Sample5.csv.gz 778.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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