|
| Status |
Public on Dec 19, 2018 |
| Title |
eMSCs_U_S5 |
| Sample type |
SRA |
| |
|
| Source name |
Human endometrial mesenchymal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
replicate: 5
tissue source and immunoselection of cells: Primary cells derived from human endometrium using SUSD antibody
passage: 6
treatment: U-Untreated/DMSO vehicle Control
|
| Treatment protocol |
eMSCs were cultured in in-house serum free culture medium with bFGF and EGF at 5% oxygen and passaged at 5000cell/cm2. At pasage 6, the cells were treated with 1mM A83-01 for 7 days with media change every 48 hours.
|
| Growth protocol |
eMSCs were cultured in in-house serum free culture medium with bFGF and EGF at 5% oxygen and passaged at 5000cell/cm2. At pasage 6, the cells were treated with DMSO vehicle control for 7 days with media change every 48 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using PureLink® RNA mini Kit (Ambion, Invitrogen) including treatment with RNase-free DNase (QIAGEN).
Sequencing libraries prepared from 1mg input RNA (depleted of ribosomal RNA) with Illumina TruSeq Poly-A mRNA Library Pro Kit protocol 15031047 RevD (Illumina, Hayward, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
18714P6U
|
| Data processing |
Quality filtering used Illumina CASAVA v1.8.2 software (Illumina, Hayward, CA) with >97% of reads having quality >Q30.
Illumina adaptor sequences were removed.
RNA sequenced reads were mapped against the Human Reference Genome GRCh38 and Ensembl 87 gene annotation using STAR (v2.5.2) with the RNAsik pipeline and manipulated with samtools (v1.3.1) and picard tools.
Gene-level counts were generated using HTseq-count (v0.6.1p1).
Genes were then filtered to those having >10 reads in at least one sample for subsequent analysis and differential expression was calculated across paired A83-01-treated and untreated samples using voom and limma (v3.26.9) via the degust interface
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of sequence fragments aligned to each gene.
|
| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Shanti Gurung |
| E-mail(s) |
shanti.gurung@hudson.org.au
|
| Organization name |
Hudson Institute of Medical Research
|
| Street address |
27-31 Wright Street
|
| City |
Clayton |
| State/province |
Vic |
| ZIP/Postal code |
Postal |
| Country |
Australia |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE115137 |
The transcriptome of human endometrial mesenchymal stem cells under TGFβR inhibition reveals improved potential for cell-based therapies |
|
| Relations |
| BioSample |
SAMN09288342 |
| SRA |
SRX4145825 |
