|
| Status |
Public on Jan 31, 2019 |
| Title |
miRNAs from spent media of flight cells, Osteogenic medium, biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
hBMSCs on board the ISS cultured in osteogenic medium
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: bone marrow mesenchymal stem cells
location: on board the ISS
medium: osteogenic
rna fraction: miRNAs from exosomes (from spent media)
|
| Growth protocol |
Standard Medium (SM): DMEM (Dulbecco’s Modified Eagle’s medium) supplemented with 12.5 mM HEPES, 10 U/mL heparin, 200 mM glutamine, 500 μg/mL streptomycin sulphate, 600 μg/mL penicillin.
Osteogenic Medium (OM): SM added with 0.1 M ascorbic acid, 10 mM b-glycerophosphate, and 10-8 M 1,25(OH)2D3 (Vit D3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used the exoRNeasy Serum/Plasma Midi Kit for miRNAs extraction from exosomes
The presence and the integrity of small RNA was assessed using an Agilent Bioanalyzer
HiSeq Rapid SBS kit v2
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FMOM_2_Exhmed_2
miRNA
|
| Data processing |
Pre-processing: Sequencing adapters removal performed with Trimmomatic (v0.32)
Pre-processing: reads in the size range of 18-50 nucleotides were selected and used for downstream analysis
Mapping: mapped against mature miRNAs in the mirBase (version 21) using BWA tool (command bwa aln; v0.7.5a)
Feature count: miRNAs expression counts were obtained with samtools (z1.2)
Differential expression analysis: differential expression analysis was performed using the edgeR (Bioconductor version 2.13). Counts were normalized and differential expression was inferred using the negative binomial distribution and a shrinkage estimator for the distribution variance of the counts.
Genome_build: mirBase: r21 mature RNA
Supplementary_files_format_and_content: raw count of reads mapping to different miRNAs for each sample
|
| |
|
| Submission date |
Jul 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Bradamante |
| E-mail(s) |
[email protected]
|
| Phone |
+390264485030
|
| Organization name |
CNR-ISTM, Institute of Molecular Science and Technology
|
| Street address |
Via Golgi 19
|
| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE100932 |
SCD – Stem Cell Differentiation on board the International Space Station [miRNA-seq on miRNAs from exosomes] |
| GSE100933 |
SCD – Stem Cell Differentiation on board the International Space Station: the problem of human bone loss |
|
| Relations |
| BioSample |
SAMN07333457 |
| SRA |
SRX2990445 |
