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Sample GSM6595087 Query DataSets for GSM6595087
Status Public on Jun 14, 2024
Title Bt549-Chip-rep1
Sample type SRA
 
Source name Cell line
Organism Homo sapiens
Characteristics tissue: Cell line
cell line: Bt-549
cell type: Breast cancer
antibody: FOXC1
genotype: FOXC1 WT
Extracted molecule genomic DNA
Extraction protocol Not provided
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Fastq trimming with trim_galore v0.6.4_dev -q 20 --paired
Mapped to hg38 with bowtie2 v2.4.1 snakemake wrapper 0.71.1/bio/bowtie2/align
Mapped reads filtered for paired end = True, mismatch NM:<=4, min fragment size >=-2000 max fragment size <=2000
Duplicate reads marked but not removed, and replicate bam files were merged and subsampled to 160 million reads, or total library size if less than 160 million reads.
Peaks called with macs2 v2.2.7.1, snakemake wrapper 0.66.0/bio/macs2/callpeak -f BAMPE -g hs --SPMR --qvalue 0.05 --keep-dup all. Peaks with fold enrichment above local background > 5 were retained for downstream analysis.
Bigwig files: bedgraph files generated with bedtools genomecov scaled by library size, converted to bw with ucsc bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: Macs2 narrowpeak files
Supplementary files format and content: Bigwig
 
Submission date Sep 21, 2022
Last update date Jun 14, 2024
Contact name Fahad Ali
E-mail(s) fahad.ali@mbru.ac.ae
Organization name Mohammed Bin Rashid University of Medicine and Health Sciences
Street address Bldg 14, Dubai Healthcare City
City Dubai
ZIP/Postal code 505055
Country United Arab Emirates
 
Platform ID GPL24676
Series (2)
GSE213840 FOXC1 in triple negative breast cancer [ChIP-seq]
GSE213841 FOXC1 in triple negative breast cancer
Relations
BioSample SAMN30950509
SRA SRX17657147

Supplementary file Size Download File type/resource
GSM6595087_Bt549-ChIP_S2.bigWig 249.4 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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