Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAseq of primary human Adipose-derived Mesenchymal Stromal Cells stimulated for 2 days with 20ng/mL IFN-gamma (versus unstimulated control) in presence of 10 nM rapamycin or DMSO (at 1:10000 dilution) as vehicle control

ABSTRACT: In order to study the impact of rapamycin on AD-MSC under inflammatory or resting conditions, primary human Adipose-derived Mesenchymal Stromal Cells (AD-MSC) at passage 1 were plated at 1.5x10^4 in MEM-alpha, 5% Human Platelet Lysate, 1% Penicillin-Streptomycin and allowed to stand for 24h. The next day, AD-MSC were stimulated for 2 days (or not) with 20ng/mL IFN-gamma in presence of 10nM rapamycin (from 10.000X stock in DMSO) or DMSO (at 1:10000 dilution) as vehicle control. After 2 days, media were removed and RNA were extracted using RNeasy kit from QIAGEN with an on-column DNAse I digestion as manufacturer's instructions. RNA intergrity number were estimated on Agilent Bioanalyzer and were all above 9 before sequencing. Libraries and RNA sequencing were performed by the Beijing Genomics Institute (BGI)

INSTRUMENT(S): DNBSEQ-T7

ORGANISM(S): Homo sapiens

SUBMITTER: Damien VERET

PROVIDER: E-MTAB-14215 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome M-bM-^@M-^\shockM-bM-^@M-^] and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, mainly siRNAs and miRNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid (genome: AB) and its allotetraploid (genome: AABB) between Brassica rapa (M-bM-^YM-^@) and Brassica nigra (M-bM-^YM-^B) in the present study.The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The high-throughput sequencing results obtained for the small RNAs showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, 320 known and 52 novel miRNAs were obtained from the parents in both the allodiploid and allotetraploid. However, quantitative real-time polymerase chain reaction (qRT PCR) analysis showed that the expression levels of the targets genes were negatively corrected with the expressed miRNAs.The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids. High throughput sequence of the parents (Brassica rapa and Brassica nigra) and their hybrids (allodiploid and allotetraploid)

Dataset Information

RNAseq of primary human Adipose-derived Mesenchymal Stromal Cells stimulated for 2 days with 20ng/mL IFN-gamma (versus unstimulated control) in presence of 10 nM rapamycin or DMSO (at 1:10000 dilution) as vehicle control

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