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| Status |
Public on Jul 07, 2022 |
| Title |
WT WGBS |
| Sample type |
SRA |
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| Source name |
Primary osteoblasts
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wild type
age: 3-day-old
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| 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.
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
May 07, 2021 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Dengfeng Ruan |
| E-mail(s) |
dfruan@zju.edu.cn
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| Organization name |
The Second Affiliated Hospital, Zhejiang University School of Medicine
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| Department |
Department of Orthopedic Surgery
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| Street address |
88 Jie Fang Road
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| City |
Hangzhou |
| State/province |
China |
| ZIP/Postal code |
310009 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN19067964 |
| SRA |
SRX10815445 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5285240_WT_allchr_methratio_steve_reduced_CG.txt.gz |
158.4 Mb |
(ftp)(http) |
TXT |
| GSM5285240_WT_allchr_methratio_steve_steve_reduced_CG_covgt3.bw |
123.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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