Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of B6/D2 Whole Brain Alternative Splicing

ABSTRACT: This dataset consists of whole brain samples from 10 B6 and 12 D2 mice, in order to assess the amount of strain-specific alternative splicing. This design consists of whole brain total RNA samples from 10 B6 and 12 D2 mice

ORGANISM(S): Mus musculus

SUBMITTER: Ted Laderas

PROVIDER: E-GEOD-27282 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Computational detection of alternative exon usage.

Laderas Ted G TG Walter Nicole A R NA Mooney Michael M Vartanian Kristina K Darakjian Priscila P Buck Kari K Harrington Christina A CA Belknap John J Hitzemann Robert R McWeeney Shannon K SK

Frontiers in neuroscience 20110513

<h4>Background</h4>With the advent of the GeneChip Exon Arrays, it is now possible to extract "exon-level" expression estimates, allowing for detection of alternative splicing events, one of the primary mechanisms of transcript diversity. In the context of (1) a complex trait use case and (2) a human cerebellum vs. heart comparison on previously validated data, we present a transcript-based statistical model and validation framework to allow detection of alternative exon usage (AEU) between diff ...[more]

PMID: 21625610

Similar Datasets

Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques

Project description:We performed gene expression profiling of total RNA from brain samples derived from BSE-infected versus non-infected cynomolgus macaques (Macaca fascicularis). Total RNA from brain samples derived from 7 BSE-infected (6 intracerebrally, 1 orally infected) versus 5 non-infected controls were compared using GeneChip Rhesus macaque Genome Array.

2014-06-10 | E-GEOD-52436 | biostudies-arrayexpress

RNA sequencing of a C57BL/6J-DBA/2J (B6.D2) congenic mouse and C57BL/6J (B6) wild-type littermates reveals cis and trans differences in gene expression

Project description:We previously utilized interval-specific congenic lines derived from C57BL/6J (B6) and DBA/2J (D2) alleles to fine map a quantitative trait locus (QTL) influencing methamphetamine (MA)- induced locomotor activity. We identified a 0.23 MB critical interval on chromosome 11 containing only two protein coding genes, Rufy1 and Hnrnph1. Notably, Rufy1 contains three missense SNPs and Hnrnph1 contains 1 SNP near the 5â UTR. In an effort to identify the molecular mechanisms that bridge genetic variation with behavior, we conducted transcriptome analysis via mRNA sequencing (RNA-seq) in a B6.D2 congenic line (chr.11: 50-60 Mb) that captures the QTL. There was an overrepresentation of cis-regulated, differentially expressed genes within the congenic interval (4 out of 92 differentially expressed genes; FDR < 0.05) and widespread genomic regulation on all autosomes. For this study, 3mm punches from both striatal hemispheres were collected and pooled from 16 mice (8 controls and 8 B6.D2 congenics), and RNA was extracted and prepared for cDNA library preparation using the Illumina TruSeq (oligo-dT; 50bp single-end reads). Samples 1-16, consisting of alternating B6 and B6.D2 congenics were run in four lanes total, with samples 1-8 run in duplicate across lanes 5 and 6 and samples 9-16 acorss lanes 7 and 8, respectively. Raw samples provided are labeled with the "CB-" prefix, followed by the sample number and the lane that it was run in is described at the tail end as "_L00#" with # being either lane 5, 6, 7 or 8. In this study, all odd samples (e.g. CB-1,3,5 etc.) are C57BL/6J littermate controls, while all even samples are B6.D2 congenics. Note that the lane 7 replicate for Sample CB-13 (CB-13_L007.fastq.gz) was not processed due to technical difficulties with the file.

2015-12-11 | E-GEOD-66366 | biostudies-arrayexpress

High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

Project description:Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Examination of allele specific expression in the brains of reciprocal crosses of F1 hybrid mice from CASTEiJ and C57BL/6J crosses. Processed data files (GenomicAligned, SNP_calls, TranscriptomeAligned, fRNAdbAligned) and README file linked below as supplementary files.

2010-07-08 | E-GEOD-22131 | biostudies-arrayexpress

Microarray of dorsal root ganglia from control and collagen antibody-induced arthritis (CAIA) male mice

Project description:Dorsal root ganglia (DRG, L3-L5) from either control mice or mice subjected to the CAIA model and treated twice weekly from day 12 with drug X or control solution were collected during the post-inflammatory phase of the model. RNA was extracted using a Qiagen RNeasy Mini Kit, subjected to GeneChip® ST Arrays (GeneChip® Mouse Gene 2.0 ST Array) analysis and assessed for presence of certain mRNA and/or group differences in mRNA levels.

2019-04-21 | E-MTAB-7853 | biostudies-arrayexpress

Transcriptome analysis of mouse cerebral cortical neural progenitor cells

Project description:Transcriptome analysis of neural progenitor/stem cells is limited by the lack of a reliable method for cell isolation. We have designed a genetic dual reporter strategy that can allow prospective isolation of cortical neural progenitor cells and their neuronal progeny form the same animals. These cells should be a good cell source for comparative global analysis. Cortical neural progenitor cells and their neuronal progeny were purified using a dual reporter strategy. The purified cells were used for comparative expression profiling.

2011-09-19 | E-GEOD-22946 | biostudies-arrayexpress

Foxp3+ regulatory T cells control psoriasiform skin inflammation by restraining a type 1 interferon driven CD8+ T cell response

Project description:Determine how regulatory T-cells restrain the cellular/transcriptional response to Imiquimod treatment in the skin (ears).

2018-06-24 | E-MTAB-6873 | biostudies-arrayexpress

Whole Genome Sequencing of splenocytes from Four Core Genotype (FCG) mice

Project description:This repository contains whole genome sequencing data from mice of the Four Core Genotypes cross. By crossing mice with both a deletion of the sex-determining factor Sry on the Y-chromosome and a transgenic insertion of Sry on Chromosome 3 , four combinations of gonadal (testis or ovaries) and chromosomal (XX or XY) are generated, namely XYSry-Chr3Sry+ (gonadal and chromosomal males), XYSry- (gonadal females, chromosomal males), XX (gonadal and chromosomal females), XXChr3Sry+ (gonadal males, chromosomal females). The transgenes were on a C57BL6 genetic background which is crossed with a CAST/EiJ female to allow for the distinction of the parental haplotypes, or on a pure-bred C57BL6 background. DNA sequencing was done on either liver or ear-punch samples.

2024-10-14 | E-MTAB-13585 | biostudies-arrayexpress

Gene expression differences between TAF4b-KO, Het and WT ovaries at 3 weeks of age

Project description:The rapid decline of ovarian function in TAF4b-null mice begins in early postnatal life and follicle depletion is completed by sixteen weeks. To uncover differences in gene expression that may underlie accelerated ovarian aging, we compared genome-wide expression profiles of three week old, pre-pubescent TAF4b-null and wild-type ovaries. Total RNA from 9, 3-week-old mice (3 wild-type, 3 TAF4b-heterozygous, 3 TAF4b-null) was obtained as described as above. RNA quality was checked using a Bioanalyzer, and concentration determined using a Nanodrop. 300 ng of each RNA sample was used in the Affymetrix Whole-transcript Sense Target Labeling Assay (Rev 3) followed by hybridization to a GeneChipÂ® Mouse Gene 1.0 ST Array. 9 GeneChips were used to provide biological triplicates of each genotype. The Affymetrix Expression Console (v 1.1) was used to normalize data and determine signal intensity (RMA-Sketch).

2010-05-20 | E-GEOD-15228 | biostudies-arrayexpress

Transcription profiling of mouse brain infected with prions in eight mouse-prion strain combinations in a systems approach to the study of prion disease

Project description:Prions cause transmissible neurodegenerative diseases and replicate by conformational conversion of normal, benign forms of prion protein (PrPC) to disease-causing PrPSc isoforms. A systems approach to disease postulates that disease arises from the pathological perturbation (genetic and/or environmental) of one or more biological networks in the relevant organ. In this regard, we tracked global (all mRNA transcripts) gene expression in the brains of eight distinct mouse strain-prion strain combinations at 8 - 10 time points throughout the progression of the disease to capture the effects of prion strain, host genetics, and PrP concentration on disease incubation time. Data are also available from http://prion.systemsbiology.net

2009-03-25 | E-MTAB-76 | biostudies-arrayexpress

Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNAseq

Project description:The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed 10 differentiated distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous novel marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSN) which have specific markers and which overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states. We measured the transcriptome of 1208 single striatal cells using two complementary approaches; microfluidic single-cell RNAseq (Mic-scRNAseq) and single cell isolation by FACS (FACS-scRNAseq) (Table S1). We sampled cells either randomly or enriched specifically for MSNs or astrocytes using FACS from D1- tdTomato (tdTom)/D2-GFP or Aldhl1-GFP mice, respectively

2016-07-15 | E-GEOD-82187 | 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