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| Status |
Public on Jul 07, 2022 |
| Title |
WT RNA-seq rep3 |
| 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 |
polyA RNA |
| Extraction protocol |
Primary osteoblasts were isolated from 3-day-old WT and TCKO mice. RNA was extracted by TRIzol (Sigma, T9424).
The RNA-seq library constructions and sequencing were utilized 3 repeats per group in WT and TCKO osteoblasts by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®(E7760L).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava software used for basecalling.
The RNA sequencing reads were aligned to GRCm38.99 Mus musculus reference genome with STAR(v2.7.0e) using a supplied set of known transcripts in GTF format (RefSeq GRCm38.99; Mus musculus, Ensembl).
Count of each gene was calculate by using featureCounts (v2.0.0).
Differentially expressed genes were calculated using DESeq2 with cutoff (Fold change greater than 2, FDR less than 0.05, and RPKM greater than 0.24 - the lower quartile), and RPKM values were calculated with a custom R script.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample，
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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 |
GPL21273 |
| Series (2) |
| GSE174046 |
RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development (RNA-Seq) |
| GSE174048 |
RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development |
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| Relations |
| BioSample |
SAMN19067936 |
| SRA |
SRX10815441 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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