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Sample GSM3444209 Query DataSets for GSM3444209
Status Public on Oct 24, 2018
Title untreated_S01
Sample type SRA
 
Source name femoral heads/knee bone explants
Organism Homo sapiens
Characteristics cell type: Mesenchymal stromal cells
treatment: untreated
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 SAMN10282885
SRA SRX4925792

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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