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Status |
Public on Jun 14, 2024 |
Title |
Bt549-Chip-rep1 |
Sample type |
SRA |
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Source name |
Cell line
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Organism |
Homo sapiens |
Characteristics |
tissue: Cell line cell line: Bt-549 cell type: Breast cancer antibody: FOXC1 genotype: FOXC1 WT
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Extracted molecule |
genomic DNA |
Extraction protocol |
Not provided
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Sep 21, 2022 |
Last update date |
Jun 14, 2024 |
Contact name |
Fahad Ali |
E-mail(s) |
fahad.ali@mbru.ac.ae
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Organization name |
Mohammed Bin Rashid University of Medicine and Health Sciences
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Street address |
Bldg 14, Dubai Healthcare City
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City |
Dubai |
ZIP/Postal code |
505055 |
Country |
United Arab Emirates |
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Platform ID |
GPL24676 |
Series (2) |
GSE213840 |
FOXC1 in triple negative breast cancer [ChIP-seq] |
GSE213841 |
FOXC1 in triple negative breast cancer |
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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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
Processed data provided as supplementary file |
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