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Sample GSM2211688

Query DataSets for GSM2211688

Status

Public on Jun 23, 2016

Title

Input_PH_WT_rep1_CHIPSeq

Sample type

SRA

Source name

Embryo 16h-18h

Organism

Drosophila melanogaster

Characteristics

genotype: WT
tissue: Embryo
age: 16-18
antibody: none

Extracted molecule

genomic DNA

Extraction protocol

Chromatin prepared from Drosophila embryos was immunoprecipitated with specific antibodies and precipitated DNA was isolated (see mat and methods for details)
Libraries were prepared according to Illumina's instructions

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2000

Data processing

Mapping - For each ChIP-seq experiment, we mapped short reads to the appropriate reference genome using Bowtie by specifying ‘-a –m 1 -best -strata’ options. Our reference genomes included the heterochromatic fraction of chromosomes and non-assembled contigs, and any read that could be mapped to more than one genomic locus was filtered from further processing.
Peak finding – For PH MACS 1,4 has been used with standard parameters, with genome size set to dm. For H3K27me3, SICER has been used with 500bp windows, 2kb as gap and FDR at 10 %
Genome_build: dm³
Supplementary_files_format_and_content: bedgraph files were generated with custom scripts from raw aligned files, bed files were generated with MACS1.4 for PH and SICER for H3K27me3

Submission date

Jun 23, 2016

Last update date

May 15, 2019

Contact name

Bernd Schuettengruber

E-mail(s)

bernd.schuttengruber@igh.cnrs.fr

Organization name

Institute de Génétique Humaine

Lab

Cavalli