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Sample GSM1600203 Query DataSets for GSM1600203
Status Public on Sep 14, 2016
Title Input-seq_in_Psc-minus_cells_replicate2 [part 1]
Sample type SRA
 
Source name Cultured cells
Organism Drosophila melanogaster
Characteristics cell line: Psc4-1
mutation: Su(z)2-1.b8
antibody: none
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 Feb 03, 2015
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)
GSE65566 Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 1)
GSE83248 Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements
Relations
BioSample SAMN03327457
SRA SRX864530

Supplementary file Size Download File type/resource
GSM1600203_Psc4-3_InputV2_extended.wig.gz 59.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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