|
| Status |
Public on Nov 04, 2019 |
| Title |
MSC83_AI_RNASeq_1_4282_4 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal Stem Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal Stem Cells (MSCs)
time point: Time Point 2
control vs differentiated: Differentiated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone-marrow derived mesenchymal stromal cells (LY-MSCs) from healthy individuals were differentiated to adipocytes following the FRCBS previously published protocol. In preparation for adipogenic differentiation cells at passage P3 were plated in 10 cm cell culture plates and grown in expansion media until they reached 70%-90% confluence , at which point the media was changed to adipogenic basal medium. Half of the culture plates were used as controls and maintained in the adipogenic basal medium until harvesting (AC samples). The other half was subjected to adipogenic differentiation (AD samples). More specifically the cells were first incubated for 3-4 days in adipogenic basal media (Timepoint 2), then the media was changed to the terminal differentiation cocktail. The media of all plates was changed twice a week and the differentiation was allowed to proceed for 3 weeks for Timepoint 3 or 4 weeks for Timepoint 4. For each donor samples were harvested at Timepoint 2 (AIC and AID: Adipocyte induced control without drugs in the media or differentiated with induction drugs), Timepoint 3 (AC1, AD1: Adipocyte control without drugs in the media or differentiated with drugs) and Timepoint 4 (AC2, AD2: Adipocyte control without drugs in the media or differentiated with drugs).
0.5 to 3 million cells were re-suspended in 500 uL TRIzol Reagent and total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA library preparations were carried out on 500 ng of RNA with RNA integrity number (RIN)>7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol. Final libraries were analyzed on a Bioanalyzer and sequenced on the Illumina HiSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
MSC83_AI_RNASeq_1
HI.4282.004.Index_14.MSC83_AI_RNASeq
|
| Data processing |
Raw reads were trimmed for quality (phred33 ≥30) and length (n≥32), and Illumina adapters were clipped off using Trimmomatic v. 0.35
Filtered reads were then aligned to the GRCh38 human reference using STAR v. 2.5.3a
Raw read counts of genes were obtained using htseq-count v.0.6.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file containing RPKM values of each sample
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Mar 14, 2021 |
| Contact name |
Elin Grundberg |
| Organization name |
CHILDREN'S MERCY HOSP (KANSAS CITY, MO)
|
| Street address |
2401 Gillham Road
|
| City |
Kansas City |
| State/province |
Missouri |
| ZIP/Postal code |
64108 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE135775 |
Gene expression analysis of mesenchymal stem cells at different stages of differentiation in to adipocytes |
| GSE136230 |
Single-cell analysis of human adipose tissue |
|
| Relations |
| BioSample |
SAMN12566739 |
| SRA |
SRX6708587 |
