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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis (PAGODA)

ABSTRACT: The extent of transcriptional diversity in mouse NPCs is likely to be influenced by a variety of unexamined factors that include programmed cell death, genomic mosaicism as well as a variety of âenvironmentalâ influences such as changes in exposure to signaling lipids. We therefore used scRNA-seq to assess a cohort of cortical NPCs from an embryonic mouse. We demonstrate that PAGODA (Pathway And Geneset OverDispersion Analysis) effectively recovers the known neuroanatomical and functional organization of NPCs, identifying multiple aspects of transcriptional heterogeneity within the developing mouse cortex that are difficult to discern by the existing heterogeneity analysis approaches. Examination of mouse NPC transcriptional heterogeneity via single cell RNA-seq

ORGANISM(S): Mus musculus

SUBMITTER: Jean Fan

PROVIDER: E-GEOD-76005 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis (PAGODA)

Project description:The extent of transcriptional diversity in mouse NPCs is likely to be influenced by a variety of unexamined factors that include programmed cell death, genomic mosaicism as well as a variety of “environmental” influences such as changes in exposure to signaling lipids. We therefore used scRNA-seq to assess a cohort of cortical NPCs from an embryonic mouse. We demonstrate that PAGODA (Pathway And Geneset OverDispersion Analysis) effectively recovers the known neuroanatomical and functional organization of NPCs, identifying multiple aspects of transcriptional heterogeneity within the developing mouse cortex that are difficult to discern by the existing heterogeneity analysis approaches.

2016-01-18 | GSE76005 | GEO

Role of Fbxo7 in dopaminergic neurons

Project description:Analysis of a conditional knockout of Fbxo7/Park15 expression in mouse brains.

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Gene expression patterns in 23 cervical samples of women having gone through different types of child birth

Project description:We performed a microarray experiment to test the hypothesis that pre-labour premature rupture of fetal membranes (PPROM) has a different underlying pathology from spontaneous premature labour with intact membranes (PTL). We thought that the different genetic signature would be detected in the cervical tissue. Our study included cervical biopsies obtained as previously described from women undergoing caesarean section (CS) following PPROM, PTL, term labour (TL) or delivering at term prior to the presentation of labour (Term no labour âTNL). After quality control of the expression arrays, any association between sample covariates was evaluated and no evidence was found of unexpected associations. The differences in expression levels for each statistical comparison were then computed. We identified genes that were differentially expressed with an adjusted pvalue < 0.01 from hypothesis testing together with a fold change >= 2. The strongest effect, i.e. the contrast with the highest number of DEGs, was observed for âTerm labour vs Term not labourâ (1,285 genes) while the contrast with the fewest DEGs was âTerm labour vs Preterm premature rupture of membranesâ (16 genes). A table showing the number of differentially expressed genes, for each comparison, can be found in the Results section of this report. We then examined the number of genes overlapping between the statistical comparisons performed (see section 2.5 of the Results) and found that the contrast âTerm labour vs Term not labourâ had a large number of DEGs in common with the five other contrasts.

2016-12-22 | E-MTAB-5354 | biostudies-arrayexpress

Proteomic profiling reveals central role of STAT signaling during retinal degeneration in the rd10 mouse model

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Transcriptional profiling by array of pancreatic ductal adenocarcinoma xenograft models

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Integrity of the short arm of nuclear pore Y-complex is required for mouse embryonic stem cell growth and differentiation

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