Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA157981 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR453186.fastq.gz | Fastqsanger.gz | |||
| SRR453187.fastq.gz | Fastqsanger.gz | |||
| SRR453188.fastq.gz | Fastqsanger.gz | |||
| SRR453189.fastq.gz | Fastqsanger.gz |
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2012-04-06 | E-GEOD-37061 | biostudies-arrayexpress
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Project description:We report the use of single-cell RNA sequencing (scRNA-seq) technique to compare the transcriptomic profiles of human breast cancer cells with high and low expression of miR-125b. Methods: MDA-MB-231(miR-125b-promo-EGFP) cells were flow sorted at maximum and minimum 5% of miR-125b expression level, and deep sequenced using Illumina HiSeq 2000. The sequencing reads that passed quality filters were mapped to the reference genome using TopHat, followed by counting of reads numbers using HTSeq Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the human DNA reference genome (build hg19) and identified 48162 transcripts in MDA-MB-231(miR-125b-promo-EGFP) cells with low and high miR-125b expression. A total of 303 transcripts showed differential expression between low and high miR-125b expression cells, with |log2 (Fold change)| ≥ 2 and adjusted p value ≤ 0.05
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Project description:We report here the expression profile of microRNAs in human neuronal differentiation in the neuroblastoma cell line SH-SY5Y. Six microRNAs were significantly upregulated during differentiation induced by all-trans¬-retinoic acid and brain-derived neurotrophic factor. We demonstrated that ectopic expression of either miR-124a or miR-125b increases the percentage of differentiated SH-SY5Y cells with neurite outgrowth. Subsequently, we focused our functional analysis on miR-125b and demonstrated the important role of this miRNA in both spontaneous and induced differentiation of SH-SH5Y cells, based on neurite outgrowth and neuronal marker expression. In human neural progenitor ReNcell VM cells, miR-125b is also upregulated during differentiation and miR-125b ectopic expression significantly promotes neurite outgrowth. To identify the targets of miR-125b regulation, we profiled the global changes in gene expression following miR-125b ectopic expression in SH-SY5Y cells. miR-125b represses 164 genes that contain the seed match sequence of the microRNA and/or predicted to be direct targets of miR-125b by conventional methods. Pathway analysis suggests that a subset of miR-125b-repressed targets antagonize neuronal genes in several neurogenic pathways, thereby mediating the positive effect of miR-125b on neuronal differentiation. We have further validated the binding of miR-125b to the microRNA response elements of ten selected targets. Together, we report here for the first time the important role of miR-125b in human neuronal differentiation. Keywords: mir125-OE/mir-scrambled control comparison & mir125-KD/mir-scrambled control comparsion
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