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Sample GSM2552035 Query DataSets for GSM2552035
Status Public on Mar 30, 2017
Title H3K27me3_in_comr_testes_Rep1
Sample type SRA
 
Source name H3K27me3_in_comr_testes
Organism Drosophila melanogaster
Characteristics genotype: comr
gender: male
age: 3 days old
tissue: adult testes
chip antibody: anti-H3K27me3 (Abcam, catalog #6002)
Growth protocol The flies were kept at 23°C
Extracted molecule genomic DNA
Extraction protocol To perform H3K27me3 ChIP-seq, we used the True MicroChIP & MicroPlex Library Preparation™ Package (Diagenode), according to manufacturer’s recommendations. 400 adult testes of comr or can homozygotes were used as a starting material for two biological replicates. Abcam anti-H3K27me3 antibodies (#6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using MicroPlex Library Preparation protocol. The libraries were sequenced on the Illumina MiSeq system.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description comr_H3K27me3_1kb_QN.txt.gz
Data processing The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with the following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample.
Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment. To build the whole genome profile, the data were processed using a 1kb sliding window, step 100 bp. Occupancy profiles were quantile normalized.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: .txt files report occupancy profiles
 
Submission date Mar 28, 2017
Last update date May 15, 2019
Contact name Petr Laktionov
E-mail(s) laktionov@mcb.nsc.ru
Organization name Institute of molecular and cellular biology SD RAS
Lab Genomics lab
Street address Lavrenitev ave 8/2
City Novosibirsk
ZIP/Postal code 630090
Country Russia
 
Platform ID GPL16479
Series (2)
GSE97127 Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [ChIP-Seq]
GSE97182 Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis
Relations
BioSample SAMN06647766
SRA SRX2677156

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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