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Sample GSM6997599 Query DataSets for GSM6997599
Status Public on Jan 27, 2023
Title MDA-MB-231 DSM OE
Sample type SRA
Source name Triple negative breast
Organism Homo sapiens
Characteristics strain: MDA-MB-231
tissue: Triple negative breast
genotype: DSM Overexpression
Growth protocol The panel of MDA_MB-231 derived cell lines (control, WT DAXX OE, and DSM OE) were cultured in complete DMEM.
Extracted molecule genomic DNA
Extraction protocol The cells were resuspended in a swelling buffer in the presence of the protease inhibitor cocktail (Sigma) and then pelleted and resuspended in the SDS lysis buffer. The lysates were transferred to a Covaris microTUBE and sonicated with an E220 Covaris Ultrasonicator. Chromatin fragmentation (~500 bps) was verified through agarose gel electrophoresis. DNA was extracted using Qiagen mini prep based on manufacturer instructions.
DNA libraries were prepared for sequencing using standard ChIP Illumina protocols
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing ChIP-seq sequencing reads (Fastq files) were mapped to the human genome (GRCh37/hg19) using Bowtie2 (Langmead and Salzberg, 2012), where option –local was specified to trim or clip unaligned reads from one or both ends of the alignment. Genome browser BedGraph tracks and read density histograms were generated using SeqMINER. Peak finding and annotation to the nearest Refseq gene promoter was performed and de novo motif discovery was carried out using HOMER (Heinz et al., 2010).
Assembly: hg19
Supplementary files format and content: matrix table for peak distritbutions
Supplementary files format and content: matrix table for region distritbutions
Submission date Jan 26, 2023
Last update date Jan 28, 2023
Contact name Daiqing Liao
Phone (352) 273-8188
Organization name University of Florida
Department Anatomy and Cell Biology
Lab 480E
Street address 2033 Mowry Rd
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
Platform ID GPL16791
Series (1)
GSE190783 DAXX genome binding/occupancy profiling by high throughput ChIP sequencing
SRA SRX19194568
BioSample SAMN32944537

Supplementary file Size Download File type/resource
GSM6997599_DSM_OE_IM9_S28_L004_R1_001.bed.gz 154.2 Mb (ftp)(http) BED
GSM6997599_DSM_OE_peak_distributions_IM9_S28_L004_R1_001.xlsx 6.1 Mb (ftp)(http) XLSX
GSM6997599_DSM_OE_region_distributions_IM9_S28_L004_R1_001.xlsx 6.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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