|
| Status |
Public on Oct 24, 2018 |
| Title |
EGF_S01 |
| Sample type |
SRA |
| |
|
| Source name |
femoral heads/knee bone explants
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mesenchymal stromal cells
treatment: EGF
|
| Treatment protocol |
Cells were allowed to adhere overnight in MSC basal medium before stimulation for 24hrs with 10 nM epidermal growth factor (EGF) alone, EGF in the presence of 10 µM IWR-1 or left untreated in 2 ml MSC basal medium.
|
| Growth protocol |
Primary human MSCs at p4 were plated into two wells of three 6 well plates in triplicate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 24hrs, media was aspirated and total cellular RNA was extracted following the manufacturer’s guidelines using a Nucleospin RNA II kit from Macherey-Nagel having pooled cells from two wells for each RNA column to increase yield.
RNA yield was quantified and checked for quality using a Nanodrop spectrophotometer before quality control and further quantification using an Agilent bioanalyser prior to RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Cufflinks_FPKMs_and_TukeyHSD_results.txt
|
| Data processing |
Illumina HiSeq 3000 sequencing
Reads were trimmed using Cutadapt v.1.8.3
Reads were aligned to version GRCh38 of the human genome using HISAT2 v 2.0.5
Transcriptomes were assembled and gene expression quantified using the Tuxedo pipeline (version 2.2.1). Transcriptome assembly, merging, quantification and normalisation to fragments per kilobase per million mapped reads (FPKM) were performed using Cufflinks, Cuffmerge, Cuffquant and Cuffnorm, respectively.
An analysis of variance model with experimental condition (Control, EGF, EGF+IWR-1) as factor was fit to the FPKM values in the R stats package, followed by Tukey HSD test to calculate adjusted p-values to estimate which groups differed.
Genome_build: Human genome GRCh38 GCA_000001405.15
Supplementary_files_format_and_content: Cufflinks_FPKMs_and_TukeyHSD_results.txt: tab-delimited text file containing Cuffnorm output, including FPKM values for each gene in all 9 samples, as well as Tukey HSD results in the form of p-values.
|
| |
|
| Submission date |
Oct 23, 2018 |
| Last update date |
Oct 24, 2018 |
| Contact name |
Katherine Newling |
| E-mail(s) |
katherine.newling@york.ac.uk
|
| Phone |
+44 (01904) 328767
|
| Organization name |
University of York
|
| Department |
Biology
|
| Street address |
Wentworth Way
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE121697 |
Epidermal growth factor activates β-catenin via integrin-linked kinase to control proliferation of mesenchymal stromal cells. |
|
| Relations |
| BioSample |
SAMN10282882 |
| SRA |
SRX4925795 |
