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Sample GSM2197635 Query DataSets for GSM2197635
Status Public on Sep 14, 2016
Title Pc_ChIP-seq_in_Su(z)12-minus_cells_replicate1 [part 3]
Sample type SRA
 
Source name Cultured cells, Su(z)12-null, Pc ChIP
Organism Drosophila melanogaster
Characteristics cell line: S12-26I3
mutation: Su(z)124
chip antibody: Pc from Poux et al., 2001
Treatment protocol None
Growth protocol Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate.
Extracted molecule genomic DNA
Extraction protocol Live cells were crosslinked with 1.8% formaldehyde for 10 min at 25C and soluble chromatin prepared as described in Schwartz et al., 2006. ChIP was done as described in Schwartz et al., 2006.
Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (New England BioLabs) following the manufacturer instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Base calling and quality score assignment were done with built-in Real-time analysis (RTA) software (Illumina).
ChIP-seq reads were aligned to the dm3 genome assembly using bowtie2 using the default parameters.
The SAM files with aligned reads were tested for strand cross-correlation using pyicos.
The SAM files were converted to wig format using pyicos. During conversion, the reads were extended based on the results of the above cross-correlation analysis.
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated using pyicos; Scores represent the number of reads overlapping each genomic position.
 
Submission date Jun 12, 2016
Last update date May 15, 2019
Contact name Yuri B Schwartz
Organization name Umeå University
Street address Byggnad 6L, NUS
City Umeå
ZIP/Postal code 90187
Country Sweden
 
Platform ID GPL16479
Series (2)
GSE83247 Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 3)
GSE83248 Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
Relations
BioSample SAMN05231709
SRA SRX1837975

Supplementary file Size Download File type/resource
GSM2197635_S12-10-Pc_extended.wig.gz 53.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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