MicroRNA expression in human brain development
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: shannon bruse
PROVIDER: E-GEOD-45126 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Despite the well-established role of the frontal and posterior peri-sylvian cortices in many facets of human-cognitive specializations, including language, little is known about the developmental patterning of these regions in human brain. We performed a genome-wide analysis of human cerebral patterning during mid-gestation, a critical epoch in cortical regionalization. A total of 345 genes were identified as differentially expressed (DE) between superior temporal gyrus (STG) and the remaining cerebral cortex (CTX). GO categories representing transcription factors were enriched in STG, while cell-adhesion and extracellular matrix molecules, were enriched in the other cortical regions. Q-PCR or in situ hybridization were performed to validate differential expression in a subset of 32 genes, most of which were confirmed. LIM domain binding 1 (LDB1), which we show to be enriched in the STG, is a recently identified interactor of LIM domain only 4 (LMO4), a gene known to be involved in the asymmetric pattering of the peri-sylvian region in the developing human brain. Protocadherin 17 (PCDH17), a neuronal cell adhesion molecule, was highly enriched in focal regions of the human prefrontal cortex. Contactin Associated Protein-Like 2 (CNTNAP2), in which mutations are known to cause autism, epilepsy and language delay, showed a remarkable pattern of anterior enriched expression in cortical regions important for human higher cognition. Importantly, a similar pattern was not observed in the mouse or rat. These data highlight the importance of expression analysis of human brain and the utility of cross-species comparisons of gene expression. Genes identified here provide a foundation for understanding molecular aspects of human-cognitive specializations and disorders that disrupt them. Experiment Overall Design: Fresh frozen human mid-gestation brains were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (University of Maryland, Baltimore, MD). After separation of the two hemispheres, tissue from STG was extracted. RNA from STG and remaining CTX was hybridized on both Agilent G4110A arrays (n=8) and Affymetrix HGU133A arrays (n=17).
2008-06-18 | E-GEOD-9335 | biostudies-arrayexpress
Project description:Human lung samples from control and Down Syndrome prenatal patients were examined for Angiogenic Factors qPCR gene expression profiling was performed to analyze the gene expression differences between human prenatal Down Syndrome patients and age matched control samples. Human lung tissue was obtained from the University of Maryland, Baltimore through its NICHD Brain and Tissue Bank for Developmental Disorders (NICH Contract #HHSN275200900011C, Ref. No. N01-HD-9-0011). The studies included in this report were examined by an institutional review board (IRB) of the University of Colorado School of Medicine and the Childrenâs Hospital Colorado and are supported through the Decedent Research Certification Program All tissues were collected, stored and distributed while maintaining strict confidentiality, meeting appropriate HIPPA standards, with oversight provided by the University of Colorado IRB. Accordingly, limited clinical data is available. Small numbers of tissue were available for study, including 5 DS and 4 control flash frozen samples for quantitative RT-PCR. Total RNA was extracted from human lung tissue using the RNAqueous Total RNA Isolation Kit (Life Technologies AM1912). Samples were DNase I treated with the Ambion TURBO DNA-free kit (Invitrogen AM1907) and tested for quality with an Agilent 2100 Bioanalyzer. Samples were reverse-transcribed with RT2 First Strand Kit (Qiagen 330401). These samples were amplified using the RT2 Profiler PCR Array Human Angiogenesis (Qiagen PAHS-024Z). Quantitative RT-PCR was performed on a LightCycler LC480 System (Roche).
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Project description:Differences in transcript splicing are well documented among tissues and between sexes in humans and other organisms. Further, splicing changes in selected genes have been reported in human and mouse brain development. Using high-throughput RNA sequencing we characterized the transcriptome-wide splicing changes occurring over the lifespan in the human brain. We found that in two brain regions, prefrontal cortex and cerebellum, as many as 37% of all expressed protein-coding multi-exon genes undergo significant splicing changes between birth and 98 years of age. Approximately 40% of these changes take place in aging. We confirmed our findings using exon arrays and PCRs and detected identified splicing changes at the protein level. We further associated distinct patterns of age-related splicing changes with expression of the corresponding splicing factors. Thus, splicing plays an important role in shaping the human brain transcriptome in both development and aging. Human post-mortem brain samples from prefrontal cortex and cerebellum from 30 individuals with ages from birth to 100 years were collected. For each five individuals of similar age RNA, extracted from dissected tissue, was pooled resulting in 5 pooled samples. Obtained RNA was hybridized with Affymetrix Human Exon 1.0 ST arrays.
2013-01-22 | E-GEOD-26586 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE17757: Gene expression data from primate postnatal brain in prefrontal cortex: time course GSE18012: miRNA expression data from human postnatal brain in prefrontal cortex: time course GSE18013: miRNA expression data from rhesus macaque postnatal brain in prefrontal cortex: time course Refer to individual Series
2010-06-09 | E-GEOD-18069 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE22521: Gene expression in primate postnatal brain through lifespan - prefrontal cortex GSE22569: Gene expression in primate postnatal brain through lifespan - cerebellar cortex Refer to individual Series
2011-12-09 | E-GEOD-22570 | biostudies-arrayexpress
Project description:Gene expression changes determine functional differentiation during development and are associated with functional decline during aging. While developmental changes are tightly regulated, regulation of aging changes is not well established. To assess the regulatory basis of age-related changes and investigate the mechanism of regulatory transition between development and aging, we measured mRNA and microRNA expression patterns in brains of humans and rhesus macaques over the entire species’ lifespan. We find that in both species, developmental and aging changes overlap in the course of lifetime with many changes found at the late age initiating in early childhood. Keywords: miRNA Age Series Keywords: Non-coding RNA profiling by high throughput sequencing Human post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the indibiual in rhesus macaque covered the whole life span fom newborn to death.
2010-06-09 | E-GEOD-18012 | biostudies-arrayexpress
Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. In this dataset, we assess the RNA detection rates using high-throughput 10x Genomics Chromium system. We mix equal volume of Control Brain RNA (3ul; FirstChoice Total Brain RNA; #AM7962) and ERCC spikes (3ul 1:4 dilution; #4456653) to make a '2x Control RNA+ERCC' master mix. The '2x Control RNA+ERCC' master mix is diluted with equal volume nuclease-free water to make '1x Control RNA+ERCC' master mix. 3ul of '1x Control RNA+ERCC' master mix is added to Chromium single cell suspension and processed as per Chromium guidelines. The sample-data relationship format (SDRF) file for this submission contains only a high-level representation of the sample, library and run information per flow cell, and not per cell. For meta-data at the level of individual cells, please refer to the supplementary file called single_cells_list.txt, which is included as part of this ArrayExpress submission.
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2013-03-22 | E-GEOD-38037 | biostudies-arrayexpress
Project description:After induction of ischemic chronic heart failure (CHF), mice exhibited depression-like behavior, in terms of increased anhedonia, and decreased both exploratory activity and interest in novelty. On histology, ischemic CHF mice showed no alterations in overall cerebral morphology. To further evaluate relevant behavioral changes found in CHF mice, RNA-sequencing analysis of prefrontal cortex and hippocampus - the brain regions, whose structural and functional alterations are associated with an increased risk for developing major depressive disorder - and of left myocardial tissue was performed in CHF vs. sham-operated animals. RNA-sequencing revealed relevant changes in hippocampal or prefrontal cortical expression of genes responsible for axonal vesicle transport (Kif5b), signal transduction (Arc, Gabrb2), limitation of inflammation (RORA; Nr4a1) and of hypoxic brain damage (Hif3a). Besides, the actual literature describes some of the genes (RORA, Gabrb2, Npas4, and Junb) being associated with depression-like behavior. Nr4a1 significantly regulated in both brain and heart tissue after induction of ischemic CHF could be a potential link and reveals the central role of inflammation in the interrelation of the brain and the failing heart. Heart failure vs. sham-operation were performed in C57BL/6 male mice. After development of chronic heart failure (CHF) 8 weeks after the operation RNA was extracted out of prefrontal cortex, hippocampus and left ventricular myocardium in both groups. RNA of 3 ischemic CHF mice versus 6 sham operated mice was pooled and further subjected to RNA sequencing. To fabricate singular pools each probe of the group equally contributed with the final amount of 2 µg RNA per pool with the result that we had 6 different pools to be further evaluated. The mRNA profile was generated by IGA Technology, Italy (http://www.igatechnology.com/) by deep sequencing, using Illumina HiSeq 2000 platform (HiSeq). CLC-Bio Genomics Workbench software (CLC Bio, Denmark) was used to calculate gene expression levels based on Mortazavi et al. (Nat Methods. 2008;5:621-628) approach.
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