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Sample GSM3771255 Query DataSets for GSM3771255
Status Public on May 17, 2019
Title UC-MSC
Sample type SRA
 
Source name cell culture
Organism Homo sapiens
Characteristics cell type: Umbilical cord MSCs
passages: 3
Growth protocol Umbilical Cord and Placenta derived cells were grown in MSC complete media and cultured in a carbon dioxide incubator at 37 ° C, 5% CO 2 , 95% humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Quality control: Raw data (raw reads) in fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. At the same time, Q20, Q30, and GC content in the clean data were calculated. All downstream analyses were based on clean data of high quality.
Read mapping to the reference genome: The reference genome and gene model annotation files were downloaded from the genome website( https://www.genome.gov/)
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene. Then, the FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: Prior to DEG analysis, for each sequenced library, the read counts were adjusted using the edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. A corrected P-value of 0.05 and absolute fold-change of 2 were set as the threshold for significant differential expression.
GO and KEGG enrichment analysis: For DEGs, Gene Ontology (GO) enrichment analysis was implemented using the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P values less than 0.05 were considered significantly enriched based on DEGs. The KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism, and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of DEGs in KEGG pathways.
Genome_build: HG38
Supplementary_files_format_and_content: counts
 
Submission date May 16, 2019
Last update date May 17, 2019
Contact name Yi Xiao
E-mail(s) yixiao9309@163.com
Phone 18826559096
Organization name Southern Medical University
Street address No. 253, Industrial Avenue, Haizhu District
City Guangzhou
ZIP/Postal code 510000
Country China
 
Platform ID GPL24676
Series (1)
GSE131355 Transcriptome sequencing analysis of Mesenchymal Stem Cells derived from the Human Placenta and Umbilical Cord
Relations
BioSample SAMN11662134
SRA SRX5849314

Supplementary file Size Download File type/resource
GSM3771255_UC.xls.gz 1.3 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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