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| Status |
Public on Jan 20, 2023 |
| Title |
hDPSCs, Ki16425, Day7 |
| Sample type |
SRA |
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| Source name |
hDPSCs
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| Organism |
Homo sapiens |
| Characteristics |
drug: Ki16425
cell type: hDPSCs
treatment: osteogenic differentiation
time: Day 7
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| Treatment protocol |
To detect the osteogenic differentiation capability of hDPSCs, they were cultured in 50 μg/mL ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich) in DMEM containing 10% FBS and 1% penicillin-streptomycin.
hDPSCs were plated in 48-well plates and treated with inhibitors in osteogenic differentiation medium, and the medium was changed every 2~3day.
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| Growth protocol |
Human dental pulp-derived mesenchymal stromal cells (hDPSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C °C
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Ki16425
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| Data processing |
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 1.3.4d, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Nov 05, 2022 |
| Last update date |
Jan 20, 2023 |
| Contact name |
SoYoung Park |
| E-mail(s) |
sypark1004@snu.ac.kr
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| Phone |
01051590787
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| Organization name |
Seoul National University
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| Street address |
Seoul, Republic of Korea,, 1 Gwanak-ro, Gwanak-gu, Seoul, 86-509
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| City |
Seoul |
| State/province |
Korea,Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE217371 |
Targeting class A GPCRs for hard tissue regeneration [RNA-seq] |
| GSE217437 |
Targeting class A GPCRs for hard tissue regeneration |
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| Relations |
| BioSample |
SAMN31619211 |
| SRA |
SRX18178216 |
| 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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