Human RNA-seq time-series of the development of seven major organs
Ontology highlight
ABSTRACT: This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from 4 weeks post conception to adulthood (including ageing).
Project description:This dataset covers the development of 6 organs (brain, cerebellum, heart, kidney, liver and testis) from embryonic day 93 to adulthood.
Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 10.5 to adulthood.
Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 13.5 to adulthood.
Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 11 to adulthood.
Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 12 to adulthood.
Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from day 10 post-conception to day 155 post-hatch.
Project description:See "Akula et al., Molecular Psychiatry in Press". RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality post-mortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false-discovery rate of <5%, we detected 5 differentially-expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, PROM1/CD133 and ABCG2 play important roles in neuroplasticity. We also show for the first time differential expression of long non-coding RNAs (lncRNAs) in BD. DE transcripts include those of SRSF5 and RFX4, which along with lncRNAs play a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology (GO) categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies. Brain transcriptome in bipolar disorder
Project description:Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by motor neuron degeneration. MATR3 is an ALS-linked gene that encodes an RNA-binding protein that is involved in alternative splicing regulation. S85C is the most commonly identified mutation in MATR3. We generated MATR3 S85C knock-in mice (of the C57BL/6 background) as a model to study ALS pathogenesis and we found that homozygous S85C mice begin to show phenotypes at around 10 weeks of age. To investigate the molecular changes that may contribute to the behavioural deficits and neurodegeneration observed in homozygous S85C mice, we performed RNA-seq on cortex, cerebellum and lumbar spinal cord tissue of wild-type, heterozygous and homozygous S85C mice (4 females per genotype) at the early symptomatic stage (8-10 weeks old). Total RNA was extracted and sent to SickKids TCAG core for mRNA library preparation, which were paired end (100 bp in length) sequenced on the Illumina NovaSeq S1 flow cell. The data obtained was aligned to mouse genome (mm10) using STAR aligner (v2.6.0), and paired-end reads mapping to exonic regions were counted using featureCounts (v1.6.3). Differential gene expression was analyzed using edgeR.
Project description:Ex vivo large-scale proteomic analysis using LC-MS/MS in postmortem brains of patients with substance use disorder and controls. Brain tissue was collected postmortem after consent from the next of kin. As part of the clinical information, medical records were obtained and a detailed psychological autopsy was performed on all participants by interviewing the next-of-kin. Information regarding the psychiatric clinical phenotypes (evidence of depression, mania, and psychosis) stressful life events, age of drug use onset, types of drugs used, smoking and drinking history, and any co-morbidities, was obtained. A diagnosis of substance use disorder was confirmed based on the psychological autopsy, detailed medical records, and review of all relevant case information by three psychiatrists at a consensus meeting. The cause of death was obtained from the medical examiner’s report and toxicological findings after death.
Project description:We report a new method for genome-wide methylation profiling that is able to probe methylation status in both single-copy DNA and interspersed repeats. This method, MethylMAPS, uses methylation-sensitive and -dependent enzymes to fractionate the genome according to methylation state. Methylated and unmethylated fragments are then sequenced with Next-Gen sequencing to map methylated and unmethylated CpG sites in the genome. We have used this method to determine the methylation status of >275 million CpG sites in human and mouse DNA from breast and brain tissues. We conclude that methylation is the default state of most CpG dinucleotides and that a combination of local dinucleotide frequencies, the interaction of repeated sequences, and the presence or absence of histone variants or modifications shields a population of CpG sites (most of which are in and around promoters) from DNA methyltransferases that lack intrinsic sequence specificity. Genome-wide methylation mapping in two normal human breast tissues, human brain tissue and mouse brain tissue.