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Series GSE159138 Query DataSets for GSE159138
Status Public on Oct 07, 2020
Title Next Generation Sequencing-based on mRNA sequencing of human adipose mesenchymal stem cells submitted to osteogenic differentiation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Next Generation Sequencing (NGS)-based mRNA sequencing (RNA-seq) has provided high-throughput measurements to analyze the transcriptome of differentiating adipose mesenchymal stem cells. We are reporting comprehensive transcriptome profiling of primarily isolated human adipose-derived mesenchymal stem cells (ADMSC) throughout consecutive culture passages using NGS-based RNA-seq method. ADMSC were isolated from human adipose tissue, cultured and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT). After osteogenic differentiation of the ADMSC, mRNA profiles of ADMSC differentiated for 1 week, 2 weeks and 3 weeks were quality controlled, and generated by deep sequencing using Illumina PE150 kits. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).
 
Overall design mRNA profiles of differentiated human adipose-derived mesenchymal stem cells after 1 week, 2 weeks and 3 weeks osteogenic differentiation
 
Contributor(s) Li S, Sack U, Li S, Simon JC, Lethaus B, Savkovic V
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Submission date Oct 06, 2020
Last update date Oct 09, 2020
Contact name Hanluo Li
Organization name University Hospital Leipzig
Department Clinic and Policlinic for Oral-, Jaw- and Plastic Face Surgery
Street address Liebigstra├če 12
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM4820191 ADMSC donor 1 1 week
GSM4820192 ADMSC donor 1 2 week
GSM4820193 ADMSC donor 1 3 week
Relations
BioProject PRJNA667749
SRA SRP286570

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE159138_ADMSC.OsteoDiffer.FPKM.exp.xls.gz 5.9 Mb (ftp)(http) XLS
GSE159138_ADMSC.OsteoDiffer.ReadsCount.xls.gz 5.1 Mb (ftp)(http) XLS
GSE159138_Quality_Report_of_pair-end_fastq_ADMSC_Osteo-Differentiation.xlsx 8.8 Kb (ftp)(http) XLSX
GSE159138_RAW.tar 5.1 Mb (http)(custom) TAR (of PDF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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