|
| Status |
Public on Jul 11, 2018 |
| Title |
PDlC-D3 mRNA |
| Sample type |
SRA |
| |
|
| Source name |
periodontal ligament stem cells, osteogenic differentiation, D3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Stem cells isolated from periodontal ligament
passage: P4
treatment: Osteogenic induction
time point: Day 3
|
| Treatment protocol |
For osteogenic induction, PDLSCs were cultured in α-MEM supplemented with 10% FBS, 100 nM dexamethasone, 200 µM L-ascorbic acid, and 10 mM β-glycerophosphate. The medium was changed every 2 days, and cells were harvested at the indicated time points.
|
| Growth protocol |
PDL tissue was collected from the middle third root of healthy premolars, cut into pieces, and digested in equal volumes of type I collagenase and dispase. Next, the isolated cells were cultured in α-Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. The cells were passaged using 0.25% trypsin and further expanded until passage 4 before they were used in the experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
miRNA: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by gel electrophoresis.
RNA-Seq: RNA libraries were prepared for sequencing using standard Illumina protocols.
miRNA-Seq: RNA libraries were prepared for sequencing using standard Ion Proton protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Processed data file: all.counts.exp.txt
|
| Data processing |
mRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20.
mRNA: Hisat2 2.0.4 mapping to reference genome.
mRNA: Count counting.
miRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA: Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCH38.p10 genome.
miRNA: Count counting.
Genome_build: hg19_GRCh38 / miRBase 21.0
Supplementary_files_format_and_content: all.counts.exp.txt: Tab-delimited text file contains counts for each mRNA sample.
Supplementary_files_format_and_content: miRNA.All.Counts.exp.txt: Tab-delimited text file contains counts for each miRNA sample.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yunfei Zheng |
| E-mail(s) |
cora2005@126.com
|
| Phone |
+861082195775
|
| Organization name |
Peking University School and Hospital of Stomatology
|
| Department |
Oral and Maxillofacial Surgery
|
| Street address |
22 Zhongguancun Avenue South, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE99958 |
Next-generation sequencing of PDLSC transcriptome |
|
| Relations |
| BioSample |
SAMN07224154 |
| SRA |
SRX2912957 |
