 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 07, 2022 |
| Title |
TCKO WGBS |
| Sample type |
SRA |
| |
|
| Source name |
Primary osteoblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: TET1/2/3 Triple knockout
age: 3-day-old
|
| Treatment protocol |
Tet1fl/fl Tet2fl/fl Tet3fl/fl mice were crossed with the Prx1-Cre strain to generate Prx1-Cre, Tet1fl/fl Tet2fl/fl Tet3fl/fl mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by DNeasy Blood & Tissue Kit (QIAGEN, 69504).
BS-seq library constructions and sequencing utilized one sample per group.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
For WGBS data analysis, raw reads were aligned to the reference GRCm38.99 Mus musculus genome using BSMAP (v 2.74) by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands(-n 1).
Methylation levels at each cytosine were then extracted with BSMAP (methratio_32unit_alt.py) scripts by allowing only unique mapped reads (-u).Methylation levels at each cytosine were calculated as #C/(#C+#T).
Genome_build: GRCm38.99
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with base site and CG methylation
|
| |
|
| Submission date |
May 07, 2021 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Dengfeng Ruan |
| E-mail(s) |
dfruan@zju.edu.cn
|
| Organization name |
The Second Affiliated Hospital, Zhejiang University School of Medicine
|
| Department |
Department of Orthopedic Surgery
|
| Street address |
88 Jie Fang Road
|
| City |
Hangzhou |
| State/province |
China |
| ZIP/Postal code |
310009 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE174047 |
RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (WGBS) |
| GSE174048 |
RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development |
|
| Relations |
| BioSample |
SAMN19067963 |
| SRA |
SRX10815446 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5285241_TCKO_allchr_methratio_steve_reduced_CG.txt.gz |
152.1 Mb |
(ftp)(http) |
TXT |
| GSM5285241_TCKO_allchr_methratio_steve_steve_reduced_CG_covgt3.bw |
110.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
