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Sample GSM5956419 Query DataSets for GSM5956419
Status Public on Jul 19, 2022
Title ChIP-seq Cp190-KO Input replicate 2
Sample type SRA
 
Source name Cultured cells
Organism Drosophila melanogaster
Characteristics cell line: CP-R6
mutation: Cp190[3]
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. Soluble chromatin was prepared and immunoprecipitation performed as described in Kahn et al. Nucleic Acids Res. 2016. 44:10132-10149
2ng of immunoprecipitated DNA were processed using NEBNext Ultra II DNA Library preparation Kit for Illumina (cat# E76455) and index oligonucleotides from NEBNext Multiplex Oligos for Illumina (cat# E7335).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Base calling and quality score assignment were done with HiSeq Control Software 2.2.58/RTA 1.18.64
Bcl to FastQ conversion was performed using None from the CASAVA software suite. The sequence read quality was reported in Sanger/phred33/Illumina 1.8+ scale.
Reads were aligned to the dm3 genome assembly using bowtie2 and the following parameters --phred33 -p 8.
Reads with MAPQ scores less than 30 were removed using samtools view -q 30
Genomic read count profiles were computed from the filtered bowtie2 alignments using pyicos convert software and the following parameters -f sam -F bed_wig -x 180 -O.
The resulted read count profiles were normalized to the number of corresponding MAPQ 30 filtered sequencing reads using custom R script
Assembly: dm3
Supplementary files format and content: Read count profiles in wig format
Supplementary files format and content: bed in dm6 transferred by UCSC liftover from above wig, example
 
Submission date Mar 16, 2022
Last update date Jul 20, 2022
Contact name Jia-Ming Chang
E-mail(s) chang.jiaming@gmail.com
Organization name National Chengchi University
Department Department of Computer Science
Street address NO.64, Sec. 2, ZhiNan Rd., Wenshan District
City Taipei
ZIP/Postal code 11605
Country Taiwan
 
Platform ID GPL23702
Series (2)
GSE198762 Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [ChIP-seq]
GSE198763 Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements
Relations
BioSample SAMN26725067
SRA SRX14474256

Supplementary file Size Download File type/resource
GSM5956419_CPR6-5_Input_q30_x180_norm_seq_depth-dm6.wig.gz 63.3 Mb (ftp)(http) WIG
GSM5956419_CPR6-5_Input_q30_x180_norm_seq_depth.wig.gz 46.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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