Unknown,Transcriptomics,Genomics,Proteomics

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Whole transcriptome analysis of postmortem human hippocampus dentate gyrus granlule cells

ABSTRACT: We investigated the transcriptome of dentate gyrus (DG) granule cells in postmortem hippocampus from 79 subjects with mental illness (schizophrenia, bipolar disorder, major depression) or non-psychiatric controls. Material for RNA-seq analysis was harvested from tissue slides using laser capture microdissection (LCM) and aRNA amplification. Equimolar amounts of triplicate aRNA samples for each of the 79 subjects were then pooled for the preparation of sequencing libraries. Sequencing libraries were prepared using Applied Biosystem's Total RNA Sequencing Kit, following the directions for Whole Transcriptome Libraries, and analyzed with an Applied Biosystems SOLiD 4 high-throughput sequencer. We compared the performance of different normalization methods (length normalization vs. noise reductin scaling), and assembled evidence for dysruption of signaling by the micro RNA miR-182 in subjects with major depression and schizophrenia.

ORGANISM(S): Homo sapiens

SUBMITTER: Ruth Kohen

PROVIDER: E-GEOD-42546 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology. Here we report the first transcriptome dynamics of single matured bovine oocytes and all stages of pre-implantation embryos developed in vivo. Surprisingly, nearly half of the bovine genome, 11,488 to 12,729 genes involved in more than 100 pathways, is expressed in oocytes and early embryos. Despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. A total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome activation occurs at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development. Using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryogenesis; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first embryonic expression profile comparison across three mammalian species, human, mouse and bovine, for which RNA-seq data are available. We found that the three species share more maternally deposited genes than embryonic genome activated genes. More importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development. This study provides the first comprehensive examination for gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development. RNA-Seq profiles from single in vivo matured oocytes and in vivo developed embryos from the 2-cell to the blastocyst stages generated using Solid RNA-seq platform.

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Whole transcriptome analysis of postmortem human hippocampus dentate gyrus granlule cells

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