Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rhesus macaque RNA-seq time-series of the development of six major organs

ABSTRACT: This dataset covers the development of 6 organs (brain, cerebellum, heart, kidney, liver and testis) from embryonic day 93 to adulthood.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Macaca mulatta

SUBMITTER: Margarida Cardoso Moreira

PROVIDER: E-MTAB-6813 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Human RNA-seq time-series of the development of seven major organs

Project description: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).

2019-02-18 | E-MTAB-6814 | biostudies-arrayexpress

Mouse RNA-seq time-series of the development of seven major organs

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.

2019-02-18 | E-MTAB-6798 | biostudies-arrayexpress

Rat RNA-seq time-series of the development of seven major organs

Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 11 to adulthood.

2019-02-18 | E-MTAB-6811 | biostudies-arrayexpress

Opossum RNA-seq time-series of the development of seven major organs

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.

2019-02-18 | E-MTAB-6833 | biostudies-arrayexpress

Rabbit RNA-seq time-series of the development of seven major organs

Project description:This dataset covers the development of 7 organs (brain, cerebellum, heart, kidney, liver, ovary and testis) from embryonic day 12 to adulthood.

2019-02-18 | E-MTAB-6782 | biostudies-arrayexpress

Chicken RNA-seq time-series of the development of seven major organs

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.

2019-02-18 | E-MTAB-6769 | biostudies-arrayexpress

RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms, and GTPase binding in bipolar disorder

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

2014-01-08 | E-GEOD-53239 | biostudies-arrayexpress

Gene expression changes in the cerebellum, cortex and spinal cord of MATR3 S85C knock-in mice at pre-symptomatic stage 8-10 weeks of age

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.

2020-08-18 | E-MTAB-8838 | biostudies-arrayexpress

Proteomics of Substance Use Disorder in the Dorsolateral Prefrontal Cortex

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.

2021-09-10 | PXD025269 | Pride

Chromatin and Sequence Features that Define the Fine and Gross Structure of Genomics Methylation Patterns

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.

2010-04-16 | E-GEOD-21242 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data