|
| Status |
Public on Jun 10, 2024 |
| Title |
E160/E308_Del_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Rib Cartilage
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Rib Cartilage
cell type: Primary Chondrocyte
genotype: E160(delta/delta);E308(delta/delta)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
approximately 50,000 cells were lysed and transposition reaction was performed with the Tn5 Transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified with Qiagen MinElute PCR Purification Kit. Then 5 cycles of PCR with custom Nextera PCR primers (from Wu and Buenrostro 2013) were conducted using NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs). Additional number of PCR cycles was determined by qPCR of the partly amplified products, following Wu and Buenrostro 2013. The PCR products were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 1.4x, right ratio: 0.5x) according to the manufacturer’sprotocol.
sequencing libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Quality control and preprocessing of ATAC-seq reads were performed using fastp.
ATAC-seq Reads were mapped to the mm9 reference sequence using Bowtie2 (ver. 2.4.4).
Duplicate reads were removed with Picard (ver. 2.20.7) and samtools (ver. 1.9). Peak calling was performed using MACS2 (ver. 2.2.4) with default parameters.
Assembly: mm9
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Jul 20, 2023 |
| Last update date |
Jun 10, 2024 |
| Contact name |
Kenji Hata |
| E-mail(s) |
hata.kenji.dent@osaka-u.ac.jp
|
| Phone |
+81-6-6879-2887
|
| Organization name |
Osaka University graduate school of dentistry
|
| Department |
Biochemistry
|
| Street address |
1-8 Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE237882 |
Regulatory mechanism of Sox9 gene expression in chondrocytes [ATAC-seq] |
| GSE237889 |
Regulatory mechanism of Sox9 gene expression in chondrocytes |
|
| Relations |
| BioSample |
SAMN36661275 |
| SRA |
SRX21112646 |
