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Sample GSM2300785 Query DataSets for GSM2300785
Status Public on Sep 02, 2016
Title yw embr input 2
Sample type SRA
Source name embryos
Organism Drosophila melanogaster
Characteristics genotype: yw
chip antibody: none
tissue: 0-4h embryos
Growth protocol Flies were raised at 23°C
Extracted molecule genomic DNA
Extraction protocol 20 ul of 0-4h embryos were used as starting material. 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 Illumina Nextera protocol.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
Description processed data file: ywAB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz
Data processing The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with 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 smoothed using a 10kb sliding window, step 1kb.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing Log2 of the ChIP to input RPM ratio smoothed using a 10kb sliding window with 1000 bp step.
Submission date Sep 01, 2016
Last update date May 15, 2019
Contact name Daniil Maksimov
Organization name MCB NSC RAS
Lab Genomics lab
Street address Lavrentjeva ave., 8/2
City Novosibirsk
ZIP/Postal code 630090
Country Russia
Platform ID GPL16479
Series (1)
GSE74908 Functional dissection of Drosophila melanogasterSUUR protein influence on H3K27me3 profile
BioSample SAMN05725331
SRA SRX2095159

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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