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Sample GSM7235228 Query DataSets for GSM7235228
Status Public on Mar 04, 2024
Title ATAC_MAC_1
Sample type SRA
 
Source name Articular cartilage
Organism Mus musculus
Characteristics tissue: Articular cartilage
cell line: Primary culture
cell type: Chondrocyte
genotype: wild type
treatment: None
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted using cell lysis buffer (IGEPAL CA-630, 1M Trizma HCl (pH 7.4), 5M NaCl, 1M MgCl2).
The extracted nuclei were used to prepare a library using a Tagment DNA Enzyme and Buffer Small Kit (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing ATAC-seq reads were quality-controlled using FastQC software.
Trimming of Nextera adapters and low-quality bases were conducted using Trimmomatic v0.39.
Trimmed reads were aligned to the mouse reference genome (GRCm39) using the Burrows-Wheeler Aligner-MEM version 0.7.17.
Multi-mapped reads, mitochondrial reads, and duplicate reads were removed with Samtools “view” function and MarkDuplicates.
After peak calling with merged aligned reads with MACS3, downstream analysis were performed with UROPA version 4.0.2 and TOBIAS version 0.13.1.
Assembly: mm39
Supplementary files format and content: Bigwig containing footprint score calculated with merged data
 
Submission date Apr 27, 2023
Last update date Mar 04, 2024
Contact name Jin-Hong Kim
E-mail(s) snumrl301@gmail.com
Organization name Seoul National University
Street address 1 Gwanak-ro, Gwanak-gu
City Seoul
ZIP/Postal code 08826
Country South Korea
 
Platform ID GPL21273
Series (2)
GSE230796 Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage [ATAC-seq]
GSE230801 Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage
Relations
BioSample SAMN34411604
SRA SRX20121622

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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