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Status |
Public on Mar 04, 2024 |
Title |
ATAC_MAC_1 |
Sample type |
SRA |
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Source name |
Articular cartilage
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Organism |
Mus musculus |
Characteristics |
tissue: Articular cartilage cell line: Primary culture cell type: Chondrocyte genotype: wild type treatment: None
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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).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
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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
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Submission date |
Apr 27, 2023 |
Last update date |
Mar 04, 2024 |
Contact name |
Jin-Hong Kim |
E-mail(s) |
snumrl301@gmail.com
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Organization name |
Seoul National University
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Street address |
1 Gwanak-ro, Gwanak-gu
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City |
Seoul |
ZIP/Postal code |
08826 |
Country |
South Korea |
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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 |
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Relations |
BioSample |
SAMN34411604 |
SRA |
SRX20121622 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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