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Series GSE116558 Query DataSets for GSE116558
Status Public on Dec 27, 2018
Title RNA-seq and ATAC-seq analysis on mesenchymal stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Mesenchymal stem cells (MSCs) are known to be heterogeneous; MSCs from different tissues show characteristic phenotypes. However, underlying molecular mechanisms of this MSC heterogeneity have not been clarified yet. In this study, to comprehensively understand transcriptome and epigenome of MSCs, we have analyzed multiple MSCs by RNA-seq and ATAC-seq.
 
Overall design Mesenchymal stem cells (MSCs) were isolated from bone marrow (femur, vertebra), lung, and adipose tissue. Same procedure was repeated three times to prepare three lines for each tissue type MSC. RNA-seq and ATAC-seq were conducted in triplicates using standard protocols.
 
Contributor(s) Shimbo T
Citation(s) 30531792
Submission date Jul 02, 2018
Last update date Mar 25, 2019
Contact name Takashi Shimbo
E-mail(s) shimbot@sts.med.osaka-u.ac.jp
Organization name Osaka university
Street address 2-2 Yamadaoka
City Suita
State/province Osaka
ZIP/Postal code 5650871
Country Japan
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (36)
GSM3242771 A_MSC.r1_S10_R1_001.170911_NB501621_0170_AHHJF7BGX3
GSM3242772 A_MSC.r2_S11_R1_001.170911_NB501621_0170_AHHJF7BGX3
GSM3242773 A_MSC.r3_S12_R1_001.170911_NB501621_0170_AHHJF7BGX3
Relations
BioProject PRJNA479329
SRA SRP151824

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
GSE116558_A_MSC.no_gcnorm_peaks.atacseq.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
GSE116558_A_MSC.r1_S10_R12_001.genes.results.txt.gz 517.5 Kb (ftp)(http) TXT
GSE116558_A_MSC.r2_S11_R12_001.genes.results.txt.gz 519.1 Kb (ftp)(http) TXT
GSE116558_A_MSC.r3_S12_R12_001.genes.results.txt.gz 518.2 Kb (ftp)(http) TXT
GSE116558_A_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph.gz 158.8 Mb (ftp)(http) BEDGRAPH
GSE116558_P_MSC.no_gcnorm_peaks.atacseq.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSE116558_P_MSC.r1_S7_R12_001.genes.results.txt.gz 520.5 Kb (ftp)(http) TXT
GSE116558_P_MSC.r2_S8_R12_001.genes.results.txt.gz 519.9 Kb (ftp)(http) TXT
GSE116558_P_MSC.r3_S9_R12_001.genes.results.txt.gz 520.0 Kb (ftp)(http) TXT
GSE116558_P_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph.gz 158.2 Mb (ftp)(http) BEDGRAPH
GSE116558_fBM_MSC.no_gcnorm_peaks.atacseq.narrowPeak.gz 1.6 Mb (ftp)(http) NARROWPEAK
GSE116558_fBM_MSC.r1_S4_R12_001.genes.results.txt.gz 516.7 Kb (ftp)(http) TXT
GSE116558_fBM_MSC.r2_S5_R12_001.genes.results.txt.gz 522.7 Kb (ftp)(http) TXT
GSE116558_fBM_MSC.r3_S6_R12_001.genes.results.txt.gz 521.3 Kb (ftp)(http) TXT
GSE116558_fBM_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph.gz 157.0 Mb (ftp)(http) BEDGRAPH
GSE116558_vBM_MSC.no_gcnorm_peaks.atacseq.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSE116558_vBM_MSC.r1_S1_R12_001.genes.results.txt.gz 516.4 Kb (ftp)(http) TXT
GSE116558_vBM_MSC.r2_S2_R12_001.genes.results.txt.gz 522.3 Kb (ftp)(http) TXT
GSE116558_vBM_MSC_R12_001_sorted.dedup.posshift_sorted.rm_blacklist.no_gcnorm.atacseq.bedgraph.gz 160.2 Mb (ftp)(http) BEDGRAPH
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