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| Status |
Public on Apr 15, 2020 |
| Title |
Sphere-2 |
| Sample type |
SRA |
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| Source name |
cultured primary dental papilla cells in 3D environment for 8 days
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: dental papilla
growth: in 3D environment
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| Growth protocol |
Monolayer cells were cultured in EpiCM basal medium supplemented with 2% fetal bovine serum(Cat#No.0010, StemCellTechnologies, USA), 1% cell growth supplement (EpiCGS, Cat#No.4152, StemCellTechnologies, USA) and 1% penicillin/streptomycin solution (Cat#No.0503, StemCellTechnologies, USA) for 14days.Primary Spheres were obtained by seeding DPCs at passage 2 onto 6-well Ultra low attachment plates (Cat#3471, Corning, USA) at a density of 1*104 cells/cm2 in basal EpiCM medium supplemented with methylcellulose(MC, Cat#M03134, StemCellTechnologies, USA) for 8days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collecteded by centrifugation and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quanlity filtering using fastp (version 0.20.0) with default parameters.
Mapping to GRCm38 using HISAT2 (version 2.1.0) with default parameters.
The expression level of each gene was quantified guided by reference annotation (Mus musculus, GRCm38.91) using FeatureCounts (v1.6.0) with parameters of "-t gene -g gene_name".
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited file include reads counts of all genes in each sample.
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| Submission date |
Oct 03, 2019 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Zhonghan Li |
| E-mail(s) |
[email protected]
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| Organization name |
Sichuan University
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| Department |
College of Life Sciences
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| Street address |
29 Wangjiang Road
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610064 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE138372 |
Regeneration of pulpo-dentinal-like complex by a group of unique multipotent CD24a positive stem cells |
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| Relations |
| BioSample |
SAMN12906193 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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