|
| Status |
Public on Aug 24, 2023 |
| Title |
Set 3_Donor 2 HC_biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrrow
condition: high confluency
cell line: primary cells
cell type: mesenchymal stromal cells
genotype: WT
treatment: nil
gender: male
|
| Treatment protocol |
Cells were seeded at two different conditions(low density and high density), cultured for a period of 7 days, before harvesting for RNAseq analysis. There are 2 conditions for each donor: low-confluency (LC) and high-confluency (HC).
|
| Growth protocol |
Human bone marrow-derived mesenchymal stromal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were trypsinized and harvested before subjected to RNA extraction. RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq stranded mRNA library following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Partek®Genomics Suite®
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Genomics Suite software based on quality score with end minimum quality level (Phred) at 20 and trimmed from 3-prime (right end). After trimming, reads less than 25bp are discarded.
Trimmed sequence reads were mapped to hg38 using STAR 2.7.8a index available in Partek Genomics Suite software.
Read count extraction and normalization with CPM (counts per million) was performed using Partek Genomics Software.
ANOVA was performed for differential expression gene analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Apr 30, 2023 |
| Last update date |
Aug 24, 2023 |
| Contact name |
Shu Hui Neo |
| E-mail(s) |
neosh@imcb.a-star.edu.sg
|
| Organization name |
A*STAR
|
| Department |
IMCB
|
| Street address |
61 Biopolis Dr, Proteos, Singapore 138673
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE231354 |
Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties |
|
| Relations |
| BioSample |
SAMN34473028 |
| SRA |
SRX20151609 |
