Gene expression profiles of 25 normal human tissues
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE8124 | GEO | 2007/11/14
SECONDARY ACCESSION(S): PRJNA101003
REPOSITORIES: GEO
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Project description:BackgroundMeasuring the quantity of miRNAs in tissues of different physiological and pathological conditions is an important first step to investigate the functions of miRNAs. Matched samples from normal state can provide essential baseline references to analyze the variation of miRNA abundance.ResultsWe provided expression data of 345 miRNAs in 40 normal human tissues, which identified universally expressed miRNAs, and several groups of miRNAs expressed exclusively or preferentially in certain tissue types. Many miRNAs with co-regulated expression patterns are located within the same genomic clusters, and candidate transcriptional factors that control the pattern of their expression may be identified by a comparative genomic strategy. Hierarchical clustering of normal tissues by their miRNA expression profiles basically followed the structure, anatomical locations, and physiological functions of the organs, suggesting that functions of a miRNA could be appreciated by linking to the biologies of the tissues in which it is uniquely expressed. Many predicted target genes of miRNAs that had specific reduced expression in brain and peripheral blood mononuclear cells are required for embryonic development of the nervous and hematopoietic systems based on database search.ConclusionWe presented a global view of tissue distribution of miRNAs in relation to their chromosomal locations and genomic structures. We also described evidence from the cis-regulatory elements and the predicted target genes of miRNAs to support their tissue-specific functional roles to regulate the physiologies of the normal tissues in which they are expressed.
| S-EPMC1904203 | biostudies-literature
Project description:Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. For the available limited collections of normal tissues from postmortal donors, there is a problem of data incompatibility, as different datasets generated using different experimental platforms often cannot be merged in a single panel. Here, we constructed and deposited the gene expression database of normal human tissues based on uniformly screened original sequencing data. In total, 142 solid tissue samples representing 20 organs were taken from post-mortal human healthy donors of different age killed in road accidents no later than 36 hours after death. Blood samples were taken from 17 healthy volunteers. We then compared them with the 758 transcriptomic profiles taken from the other databases. We found that overall 463 biosamples showed tissue-specific rather than platform- or database-specific clustering and could be aggregated in a single database termed Oncobox Atlas of Normal Tissue Expression (ANTE). Our data will be useful to all those working with the analysis of human gene expression.
| S-EPMC6478850 | biostudies-literature
Project description:The data set submitted here contains the raw SNP genotyping data obtained from the analysis of 24 biparental segregating maize (Zea mays L.) populations and their respective parents. The processed and filtered data were used to construct genetic linkage maps which we used in our study of variation of recombination rate in maize. In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation. In our study, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotyped 23 doubled-haploid populations derived from crosses between these lines with a 50k-SNP array and constructed high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtained the recombination rates along chromosomes specific to each population. We identified significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework revealed a negative association between recombination rate and interference strength. To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.
2013-09-05 | GSE50558 | GEO
Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues. Unpaired experiments, breast tumor tissues vs. breast non-tumor tissues. Biological replicates: 8 breast cancer tissue replicates, 8 breast non-tumor tissue replicates.
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Project description:We performed tiling array experiments to examine whole genome expression in human tissues. We investigated tissue specificity and association between evolutionary sequence conservation and transcription. A total of 22 tissues (bone marrow, cerebellum, colon, cortex, fetal brain, heart, kidney, liver, lung, pancreas, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea and uterus) and 2 cell lines (HeLa and SH-SY5Y) were examined in 36783546 regions of the Human genome in this study. Keywords: whole genome transcription, tiling array, non-coding transcripts, tissue specificity
2013-12-31 | GSE18490 | GEO
Project description:To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. Direct bisulfite sequencing showed widespread methylations occurred in intragenic regions of WT1, PAX6 and ITGA4 genes and promoter region of OTX2 in breast cancer tissue. COBRA assay in independent tumor and non-tumor samples confirmed that WT1, OTX2 and PAX6 genes were hypermethylated in breast cancer tissues. To explore the relationship between methylation and gene expression, gene expression profiling analysis was performed in 8 breast tumor tissues and 8 non-tumor breast tissues. We found that some hypermethylated genes in breast cancer were not expressed in breast tissues. RT-PCR assay showed that WT1 and PITX2 were only weakly expressed in the breast tumor tissues and weren’t expressed in most non-tumor breast tissues. OTX2 and PAX6 weren’t expressed in both breast tumor tissues and non-tumor tissues. Unpaired experiments, breast tumor tissues vs. breast non-tumor tissues. Biological replicates: 8 breast cancer tissue replicates, 8 breast non-tumor tissue replicates.
2011-11-11 | E-GEOD-33447 | biostudies-arrayexpress
Project description:Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. There is a shortage now of the gene expression data for human healthy tissues. The available data can either lack biological replicates or represent tissues adjacent to tumors removed during surgery that have signs of pathology and inflammation. For the available limited collections of normal tissues from post mortal donors, there is a problem of data incompatibility, as different datasets were generated using different experimental platforms and cannot be merged in a single panel. Here, for the first time, we construct and deposited a gene expression database of normal human tissues based on uniformly screened original sequencing (Illumina HiSeq 3000) data. A total of 148 solid tissue samples representing 20 organs were taken from post-mortal human healthy donors killed in road accidents no later than 36 hours after death. Blood and bone marrow samples were taken from 6 and 11 healthy volunteers respectively. The materials were collected since 2012 and stored until gene expression profiles were obtained by using the same reagents and protocols. Data consistency was confirmed by hierarchical clustering and principal component analysis (PCA). Our data can be useful to all those working with the analysis of human gene expression.
2018-10-04 | GSE120795 | GEO
Project description:Mammalian target of rapamycin (mTOR) is a key controller of cell growth and proliferation in normal tissues and solid tumors. In the present study, an immunohistochemical analysis of the expression pattern of phosphorylated mTOR (p-mTOR) was performed in human normal fetal and adult tissues and various carcinoma tissues. p-mTOR expression showed tissue and cell type specificity in normal and cancer tissues. In normal fetal and adult tissues, p-mTOR staining was observed in the intestinal crypt, intrahepatic bile ductule, pancreatic duct, distal nephron of the kidney, umbrella cell of urothelium, mesothelial cell, and choroid plexus. In cancer tissues, p-mTOR expression was higher in adenocarcinoma than in other types of cancers, in metastatic cancer than in primary cancer, and in the forefront of the infiltrating cancer cells. These results suggest that p-mTOR is implicated not only in cell proliferation but also in tubular morphogenesis in normal and cancer tissues. In addition, mTOR activation appears to be associated with cancer cell invasion and migration in solid tumors.
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Project description:Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of human gene regulatory elements in diverse cell types and tissues in the human body, we applied single cell chromatin accessibility assays to 25 distinct human tissue types from multiple donors. The resulting chromatin maps comprising ~500,000 nuclei revealed the status of open chromatin for over 750,000 candidate cis-regulatory elements (cCREs) in 54 distinct cell types. We further delineated cell type-specific and tissue-context dependent gene regulatory programs, and developmental stage specificity by comparing with a recent human fetal chromatin accessibility atlas. We finally used these chromatin maps to interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues and organ systems.
2021-02-16 | GSE165659 | GEO
Project description:The aim of the present study was to compare the gene expression profiles in aortic dissection (AD) and healthy human aortic tissue samples by DNA microarray analysis in order to screen the differential genes. In total, five AD and four healthy aortic specimens were selected; the total RNA was extracted and reverse transcribed into cDNA and in vitro transcribed into aRNA, followed by microarray hybridization for analysis. Thereafter, the transcription levels of six differential genes, myosin light chain kinase (MYLK), polycystin 1, transient receptor potential channel interacting (PKD-1), myosin heavy chain 11 (MYH11), superoxide dismutase 3, extracellular (SOD3), filamin A (FLNA), and transgelin (TAGLN), screened from the expression profiles were quantitatively verified. Compared with the healthy aortic specimens, a total of 1,661 genes in the AD group demonstrated more than 2-fold differential expression, of which 997 genes were upregulated and 664 genes were downregulated. Thereafter, six AD-associated genes that showed downregulation in the microarray assay were selected for quantitatively verifying the gene transcription level using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which confirmed their downregulation compared with the healthy aortic tissue genes; of the six genes, the expression levels of MYLK, PKD-1, MYH11, SOD3 and TAGLN were significantly downregulated (P<0.05), while the expression of FLNA was not significantly downregulated (P>0.05). Thus, whole genome microarray may be used to screen differentially expressed genes between AD and healthy aortic tissues. When used in combination with RT-qPCR validation, this method may provide novel strategies for investigating AD.
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