|
| Status |
Public on Nov 01, 2022 |
| Title |
ATAC-seq, control, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell type: Osteoclast Precursor Cells
treatment: M-CSF
|
| Growth protocol |
Monocytes were obtained from peripheral blood using anti-CD14 magnetic beads. Monocyte-derived osteoclast precursors (OCPs) were obtained by culturing for 1 day with 20 ng ml-1 of M-CSF in a-MEM medium supplemented with 10 % fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To prepare nuclei, 50,000 cells were spun at 500g for 5 min. Cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Remaining nuclei were spun at 500g for 10 min in a refrigerated centrifuge.
The nuclei pellet was suspended in the transposase reaction mix (Illumina). The samples were purified with Qiagen MinElute kit. Library fragment amplification was done with 1× NEB next PCR master mix and custom Nextera PCR primers. The libraries were purified with Qiagen PCR cleanup kit. Libraries were amplified for a total of 10–13 cycles.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ATAC-seq read files were first quality-checked with Fastqc v0.11.9.
If necessary, adapter sequences were trimmed with Skewer v0.2.2.
The reads were then mapped to hg19 with Bowtie2 v2.3.5.1, and further filtered and position-sorted with Samtools v1.10.
The ATAC-seq peak calls were performed with HOMER v4.11 default parameters.
Peak files were created with HOMER.
Assembly: hg19
Supplementary files format and content: gzip-compressed file containing HOMER peak call results
|
| |
|
| Submission date |
May 19, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Kibyeong Kim |
| Organization name |
Yonsei University
|
| Street address |
50-1, Yonsei-ro, Seodaemun-gu
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE203354 |
Chromatin Accessibility Profiling of Osteoclasts Precursor Cells |
| GSE203587 |
Epigenetic and Transcriptomic Profiling in Developing Osteoclasts |
|
| Relations |
| BioSample |
SAMN28544829 |
| SRA |
SRX15369736 |
