|
| Status |
Public on May 18, 2022 |
| Title |
hMSC-hTERT20_Day7_R3 |
| Sample type |
SRA |
| |
|
| Source name |
mesenchymal stromal cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: marrow stromal cell
differentiation: Day_7_osteogenic_differentiation
|
| Treatment protocol |
Cells were seeded at 1x106 cells per 100 mm dish and grown to 90% confluence. To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone and 100ng/ BMP2. Cells were harvested at defined time points (0, 7, 14 days) and stored at -80C in TRIzol.
|
| Growth protocol |
Human immortalized MSCs (hMSC-hTERT20) were grown in ascorbic acid-free alpha-MEM supplemented with 16.5% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Trizol with DNase treatment using the Direct-zol RNA mini-prep kit (Zymo Research #R2050).
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) using standard protocols.
Barcoded libraries were loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the The Vermont Integrative Genomics Resource (VIGR).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
The reads were aligned to hg38 with STAR (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation v37.
Genome_build: Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R studio.
Supplementary_files_format_and_content: Tables showing normalized counts from DESeq2 analysis.
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
May 18, 2022 |
| Contact name |
Jonathan AR Gordon |
| E-mail(s) |
Jonathan.A.Gordon@uvm.edu
|
| Organization name |
University of Vermont
|
| Department |
Biochemistry
|
| Street address |
89 Beaumont Ave Given E209
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE183931 |
Transcriptome profilng of hMSC-hTERT20 cells undergoing osteogenic differentiation |
|
| Relations |
| BioSample |
SAMN21386861 |
| SRA |
SRX12136101 |
