|
| Status |
Public on Nov 29, 2021 |
| Title |
MeDIP-Seq Tet2Rank–/–; Tet3aRank+/– osteoclasts rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Tet2Rank–/–; Tet3aRank+/– osteoclasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow-derived osteoclasts
gender: Male
strain: C57BL/6
|
| Treatment protocol |
Bone marrow cells derived from mice were seeded and cultured in alpha-MEM with 10%FBS containing M-CSF. After 2 days, adherent cells were used as bone marrow-derived monocyte/macrophage precursor cells (BMMs). The BMMs were further cultured in the presence of RANKL and M-CSF to generate osteoclasts.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared from cultured cells using the GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich) according to the manufacturers’ instructions.
Genomic DNA was sonicated to 150 bp fragments with Covaris (Covaris). Methylated DNA was enriched using MEDIP Kit (Active Motif) according to manufacturer’s protocol. The illumina libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems) and TruSeq DNA UD Indexes (Illumina) according to manufacturer’s instructions. Paired-end sequencing (100 bp x 2) was performed using HiSeq3000 (Illumina).
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Tet2Rank–/–; Tet3aRank+/– osteoclasts rep1
|
| Data processing |
Sequenced reads were trimmed with Trim Galore and mapped to the mouse genome (mm10) with Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Aug 12, 2020 |
| Last update date |
Nov 29, 2021 |
| Contact name |
Keizo Nishikawa |
| Organization name |
Graduate School of Life and Medical Sciences
|
| Department |
Medical Life Systems
|
| Lab |
Keizo Nishikawa
|
| Street address |
1-3, Tatara Miyakodani
|
| City |
Kyotanabe |
| State/province |
Kyoto |
| ZIP/Postal code |
610-0394 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE156128 |
Effect of TET deletion on the global DNA methylation status of osteoclasts (MeDIP-Seq) |
| GSE156130 |
Effect of TET deletion on the global DNA methylation status of osteoclasts |
|
| Relations |
| BioSample |
SAMN15803825 |
| SRA |
SRX8934833 |
