|
| Status |
Public on Jun 18, 2022 |
| Title |
Old biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
MSCs harvested from bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: MSCs harvested from bone marrow
cell line: Primary mouse MSCs
cell type: mesechymal stem cells
genotype: C57BL6
treatment: no treatment
|
| Treatment protocol |
Replicates of 105 old MSCs were cultured separately or in co-culture with young MSCs for 7 days using a 0.4µm Transwell system in 6-well plates (Corning) which allow transfer of soluble paracrine factors released by the cells but not of the cells themselves.
|
| Growth protocol |
All cells were incubated at 37°C in 5% CO2. MSCs were expanded in culture in alpha-MEM basal medium (Stemcell Technologies Tukwila WA) supplemented with 20% FBS (Gibco Invitrogen Carlsbad CA) 120 units/mL Penicillin 100 mcg/mL streptomycin and 2mM L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNAeasy Mini kit and followed QiaCube miRNeasy mini protocol with on column DNase I digestion
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Old MSCs day 7
|
| Data processing |
The open source Galaxy pipeline was used for data processing and analysis
Raw sequencing reads were aligned to the UCSC mm10 genome using HISAT2
Transcript assembly with StringTie
Alignment quantification with featureCounts
Count normalization and differential expression analyses with DESeq2 and Genesis
Assembly: UCSC mm10
Supplementary files format and content: tab delimited text files with normalized gene expression
|
| |
|
| Submission date |
May 31, 2022 |
| Last update date |
Jun 18, 2022 |
| Contact name |
George Hung |
| Organization name |
Yale University
|
| Street address |
300 George Street Room 741
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE205205 |
Paracrine-Mediated Rejuvenation of Aged Mesenchymal Stem Cells |
|
| Relations |
| BioSample |
SAMN28786376 |
| SRA |
SRX15529019 |
