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Sample GSM5629082 Query DataSets for GSM5629082
Status Public on Jan 01, 2022
Title BMSCs, Ost_ASA1
Sample type SRA
 
Source name BMSCs, Ost_ASA
Organism Rattus norvegicus
Characteristics cell type: Bone mesenchymal stem cells (BMSCs)
strain: Sprague-Dawley
tissue: Bone marrow
treatment: cultured in the osteogenic differentiation basal medium with aspirin
Treatment protocol Cultured in the adipogenic/osteoblastic Differentiation Basal Medium with or without aspirin
Growth protocol BMSCs at passage 3-6 were seeded in 10cm-diameter culture dish at a density of 2×104cells/cm2, and cultured in Growth Medium in 5%CO2, 37°C circumstance until they reached 100% or exceeded 100% confluency.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIZOL according to the manufacturer’s protocol. RNA purity was checked using the NanoPhotometer® spectrophotometer. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer . RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system .A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava2.19 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: readcount.txt
 
Submission date Oct 16, 2021
Last update date Jan 01, 2022
Contact name Xinpeng Liu
E-mail(s) liuxinpenglxp@sina.com
Phone 15545469218
Organization name Southern Medical University
Department StomatologicalHospital
Street address 157 health care road, nangang district, Harbin
City Guangzhou
State/province Guangdong
ZIP/Postal code 510280
Country China
 
Platform ID GPL24688
Series (1)
GSE186026 Transcriptomic analyses of the anti-adipogenic and pro-osteoblastic effects of aspirin in rat bone mesenchymal stem cell
Relations
BioSample SAMN22346326
SRA SRX12645720

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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