Project description:m6A-seq was performed on 4 brain regions (cortex, cerebellum, hypothalmus and hippocampus) of 2 week, 4 week, 6 week, 26 week and 52 week old BL6 mice. m6A profiling was also performed on human adolescent and old brain tissue (region BA9). m6A-seq was also performed on WT and 5xFAD mice (Alzheimer).
Project description:This data set consists of tissue-specific RNA-seq reads from 14 different tissues from a single female adult olive baboon (Papio anubis): bone marrow, brain cerebellum, brain frontal cortex, brain pituitary, brain temporal lobe, colon, heart, kidney, liver, lymph node, spleen, lung, skeletal muscle and thymus. The data set was generated by the non-human primate reference transcriptome resource (NHPRTR) project (http://nhprtr.org/), and was first made public on 14 Jan 2014.
Project description:Expression of known and predicted genes in tissues of Gallus gallus (chicken) pooled from multiple healthy individuals. Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps. Tissues: Bursa of Fabricius, Cerebellum, Cerebral cortex, Eye, Femur with bone marrow, Gallbladder, Gizzard, Heart, Intestine, Kidney, Liver, Lung, Muscle, Ovary, Oviduct, Skin, Spleen, Stomach, Testis, Thymus
Project description:In this study we have employed RNA seq on ten different tissues including four brain tissues from two boars to gain a understanding of the differential variations in transcriptional profiles for these tissues consisting of occipital cortex, frontal cortex, hypothalamus and cerebellum along with such diverse tissues as heart, spleen, liver, kidney, lung and musculus longissimus dorsi. This has enabled us to perform comparative gene expression analysis of brain regions versus non-brain tissues along with inter-brain tissue comparisons. Hence, we have tested for differentially expressed genes and isoforms, differential splicing, transcription start sites (TSS), and differential promoter usage between all ten porcine tissues.
Project description:The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of these tissues. Toward this end, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928 Human DNA methylation Beadchip v1.2 was used to obtain n=64 Illumina DNA methylation arrays from 30 tissues. For each of the following tissues, we obtained at least 2 replicates: adipose, adrenal gland, aorta, bone, bone-marrow, breast, buccal cells, cartilage, cerebellum, colon, diaphragm, esophagus , frontal cortex, kidney, heart, hippocampus, liver, lung, lymph node, midbrain, muscle, occipital cortex, pancreas, pericardium skin, spleen, stomach, temporal cortex, thyroid, whole blood.
Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates
Project description:We used microarray expression profiling to assess protein-coding and non-coding gene expression across 8 brain samples and 7 other human tissues. We measured commercial human cDNA samples from 15 tissues: cerebellum, brain stem, frontal cortex, occipital cortex, parietal cortex, fetal brain, whole adult brain, colon, heart, kidney, liver, lung, breast and adrenal gland
Project description:4 samples from 9 brain regions Brain tissue from the New South Wales Tissue Resource Centre, 9 brain regions, 4 samples each: 1 male alcoholic, 1 female alcoholic, 1 male control, 1 female control. Brain regions: pre-frontal cortex, cerebral cortex, visual cortex, thalamus, hippocampus, amygdala, caudate nucleus, putamen, cerebellum
Project description:Survey of gene expression in ten common inbred strains of laboratory mouse. Seven brain regions examined: amygdala, basal ganglia, cerebellum, frontal cortex, hippocampus, cingulate cortex, olfactory bulb. Experiment Overall Design: Tissue from three animals was pooled on each array. Three biological replicates per strainxregion condition. Animals were 4-5 weeks of age.
Project description:DNA methylation data from human tissues: 5 samples each of normal liver, frontal cortex, spleen and colon. 5 samples of colon tumor.
