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Sample GSM5597029 Query DataSets for GSM5597029
Status Public on Jun 15, 2022
Title SOX9OE_SOX9CUT&RUN_72h
Sample type SRA
 
Source name Umbilical vein endothelial cells
Organism Homo sapiens
Characteristics cell line: HUVEC
transduced with: SOX9 expression plasmid
cut&run/tag antibody: SOX9 (AB5535, Millipore)
Growth protocol HUVECs were cultivated in Medium 200 (Thermo Fisher Scientific) supplemented with 2% low serum growth supplement and 1% Penicillin Streptomycin.
Extracted molecule genomic DNA
Extraction protocol CUT&RUN, CUT&Tag, ATAC-seq
NEBnext DNA Ultra ii (New England Biolabs)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing Library strategy: CUT&RUN
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format
 
Submission date Sep 24, 2021
Last update date Jun 15, 2022
Contact name Bettina Maria Fuglerud
E-mail(s) bfuglerud@bccrc.ca
Organization name BC Cancer
Street address 675 W 10th Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z 1L3
Country Canada
 
Platform ID GPL30173
Series (1)
GSE155282 Chromatin profiling of HUVECs
Relations
BioSample SAMN21615304
SRA SRX12335625

Supplementary file Size Download File type/resource
GSM5597029_SOX9OE_SOX9CUT_RUN_72h.bigwig 136.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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