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Sample GSM6605928 Query DataSets for GSM6605928
Status Public on Mar 13, 2023
Title 4T1 dnMCAK ATAC biol rep 2
Sample type SRA
 
Source name 4T1
Organism Mus musculus
Characteristics strain: BALB/c
cell line: 4T1
cell type: 4T1 TNBC Breast Cancer Cells
overexpression: dnMCAK
Growth protocol 4T1 cells were grown in RPMI media supplemented with 10% FBS and 1X Pen-Strep in 245x245 mm dish (Corning Corning™ TC-Treated Culture Dishes)
Extracted molecule genomic DNA
Extraction protocol Extraction was performed according to Buenrostro et. al. 2015
Library prepared according to Buenrostro et. al. 2015
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were mapped to mm10 using bowtie2 with the following parameters: -t -X2000 --no-mixed --no-discordant. Reads were filtered based on -F 1804 -q 30 using samtools and the MarkDuplicates function in Picard tools was used to remove PCR duplicates. Peak calling was done using macs2 callpeak function with the following parameters: -f BAM -g hs --nomodel --shift 37 --extsize 73 --keep-dup all -B --SPMR --call-summits -q 1e-2. Summit of peaks were extended by 250bp and merged across samples. IGVtools count function was used to generate TDF files for visualization.
Assembly: mm10
Supplementary files format and content: bed, tdf, bigwig
 
Submission date Sep 29, 2022
Last update date Mar 13, 2023
Contact name Albert S Agustinus
Organization name Memorial Sloan Kettering Cancer Center
Street address 408 East 69th Street, Room 419-G
City New York
State/province New York
ZIP/Postal code 10021
Country USA
 
Platform ID GPL24247
Series (2)
GSE186589 Epigenetic dysregulation from chromosomal transit in micronuclei
GSE214448 Epigenetic dysregulation from chromosomal transit in micronuclei [ATAC-Seq]
Relations
BioSample SAMN31093500
SRA SRX17748700

Supplementary file Size Download File type/resource
GSM6605928_DNMCAKB_IGO_13029_C_5_S99_L002.umap.gsorted.filtered.bw 123.4 Mb (ftp)(http) BW
GSM6605928_DNMCAKB_IGO_13029_C_5_S99_L002.umap.gsorted.filtered.tdf 219.3 Mb (ftp)(http) TDF
GSM6605928_DNMCAKB_IGO_13029_C_5_S99_L002_summits_250ext_q1e6_nochrM_merged.bed.gz 168.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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