Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deep sequencing of the murine olfactory receptor neuron transcriptome

ABSTRACT: The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome.

ORGANISM(S): Mus musculus

SUBMITTER: Ninthujah Kanageswaran

PROVIDER: E-GEOD-53793 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Deep sequencing of the murine olfactory receptor neuron transcriptome.

Kanageswaran Ninthujah N Demond Marilen M Nagel Maximilian M Schreiner Benjamin S P BS Baumgart Sabrina S Scholz Paul P Altmüller Janine J Becker Christian C Doerner Julia F JF Conrad Heike H Oberland Sonja S Wetzel Christian H CH Neuhaus Eva M EM Hatt Hanns H Gisselmann Günter G

PloS one 20150115 1

The ability of animals to sense and differentiate among thousands of odorants relies on a large set of olfactory receptors (OR) and a multitude of accessory proteins within the olfactory epithelium (OE). ORs and related signaling mechanisms have been the subject of intensive studies over the past years, but our knowledge regarding olfactory processing remains limited. The recent development of next generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. ...[more]

PMID: 25590618

Similar Datasets

Ion Transporter NKCC1 - Modulator of Neurogenesis in Murine Olfactory Neurons

Project description:Olfaction is one of the most crucial senses for vertebrates regarding foraging and social behavior. Therefore, it is of particular interest to investigate the sense of smell, its function on a molecular level, the signaling proteins involved in the process and the mechanism of required ion transport. In recent years, the precise role of the ion transporter NKCC1 in olfactory sensory neuron (OSN) chloride accumulation has been a controversial subject. NKCC1 is expressed in OSNs and is involved in chloride accumulation of dissociated neurons, but it had not been shown to play a role in mouse odorant sensation. To characterize transporter gene expression in NKCC1-/- mice, we examined the OE gene profile (Supplementary Table 1) using Illumina RNA-Seq to generate OE transcriptomes from NKCC1-/- and wild type mice. We analyzed RNA from OEs of male and female NKCC1+/+ (12 ¬± 1 weeks) and NKCC1-/- mice (16.5 ¬± 3.5 weeks, NMRI background); each RNA sample was prepared from an OE pool of 4 (mixed-gender pool RNA isolation) or 2 (gender RNA pool) different mice for each condition. Our data demonstrated the absence of a highly expressed ion transporter that could compensate for NKCC1. The Illumina RNA-Seq protocol was utilized. In total, we amplified and sequenced up to 38 million 101 nt-long fragments from murine NKCC1+/+ and NKCC1-/- adult OEs.

2015-05-07 | E-GEOD-65388 | biostudies-arrayexpress

Deep sequencing of the murine olfactory receptor neuron transcriptome

Project description:The recent development of next-generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice

2015-01-21 | GSE53793 | GEO

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq]

Project description:Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both "tetra-on" and corresponding "tetra-off" iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells. Examination of the mRNA expression in 13 cell types

2013-12-06 | E-GEOD-36290 | biostudies-arrayexpress

Single Cell Sequencing Identifies Key Epigenetic Regulators in Nuclear Transfer Mediated Reprogramming [RNA-seq]

Project description:Differentiated cell can be reprogrammed into totipotent embryo through somatic cell nuclear transfer (SCNT). However, this process is highly inefficient and most cloned embryos arrest at certain developmental stages. Through single cell sequencing combined with embryo biopsy, here we generate a global map of DNA methylome and RNA transcriptome for SCNT embryos with distinct developmental fates. We subsequently demonstrate that the unfaithful reactivation of two histone demethylases, Kdm4b and Kdm5b, accounts for the arrest of cloned embryos at 2-cell and 4-cell stage, respectively. Ectopic expression of Kdm4b and Kdm5b in SCNT can remove H3K9me3 barrier, restore the transcription profile and facilitate the blastocyst developmental efficiency over 95%. Moreover, these cloned embryos can further support full-term development and the derivation of SCNT-embryonic stem cells with greater efficiency. Our study reveals that histone methylation reset is crucial for the development of SCNT embryos, which provides a clue to further improve therapeutic cloning. For SCNT embryos or injected SCNT embryos 3-8 replicates were performed for each stage . As the control, 3-6 replicates were performed for each stage of wild type samples

2016-05-17 | E-GEOD-70605 | biostudies-arrayexpress

Compensatory cis-trans regulation of mouse liver gene expression

Project description:Two inbred mouse strains, C57BL/6J and CAST/EiJ, were crossed to generate both initial and reciprocal F1 crosses. For each genetically distinct class of mice (F0 C57BL/6J, F0 CAST/EiJ, F1i - C57BL/6J x CAST/EiJ, F1r - CAST/EiJ x C57BL/6J, where the male parent is listed first), samples were collected from a single lobe of the liver from 6 male mice between the ages of 4 and 6 months. The 24 samples were then processed to generate strand-specific RNA-seq libraries, which were sequenced on the Illumina GAII platform using 72bp paired-end reads.

2012-09-07 | E-MTAB-1091 | biostudies-arrayexpress

Transcription profiling of mouse olfactory epithelium from heterozygous and homozygouse OMP-GFP animals

Project description:OMP is expressed only in mature olfactory sensory neurons, arguing that its function is specially suited to the needs of OSNs. However none of the properties of OMP suggest any direct role in regulating gene expression in OSNs. Our data confirms that gene expression in the olfactory epithelium of mice lacking OMP is indistinguishable from mice expressing OMP. We used affymerix M430v2.0 gene chips to cover as much of genome as possible and observed no statistically significant differences in mRNA abundance between the two genotypes.These results imply that OMPs ability to regulate signal transduction with in OSNs has little effect on gene expression and that its ability to promote mitosis in neighbouring cells (under culture conditions) is insufficiently active under normal laboratory housing conditions to generate detectable differences in gene expression patterns. Experiment Overall Design: The overall design of the experiment is to undertand the effect of OMP (olfactory marker protein) on gene expression in the olfactory epithelium. We isolated the olfactory epithelium from homozygous and heterozygous OMP-GFP mice, extracted the RNA and hybridized on to the mouse expression set 430 2.0 Chip.

2008-06-13 | E-GEOD-4927 | biostudies-arrayexpress

Effect of OMP on gene expression in the olfactory epithelium

2007-04-30 | GSE4927 | GEO

Molecular architecture of transcription factor hotspots in early adipogenesis

Project description:Here, we have used digital genomic footprinting to precisely define protein localization for several adipogenic transcription factors at a genome-wide level. In combination with ChIP-seq data, these analyses reveal novel molecular insight into the organization of transcription factors at hotpot regions, which provides a new framework for understanding transcription factor cooperativity on chromatin. Digital genomic footprinting and gene expression in 3T3-L1 pre-adipocytes by high throughput sequencing.

2014-05-08 | E-GEOD-57415 | biostudies-arrayexpress

RNASeq data from OMP-52M51 acute treated T-ALL PDX mice

Project description:We recently demonstrated that a human Notch1-specific neutralizing antibody (OMP-52M51) was very effective in T-ALL patient derived xenografts (PDX) bearing NOTCH1/FBW7 mutations. To evaluate the transcriptomic downstream effects of anti-NOTCH1 therapy, we perform RNA-Seq analysis in leukemia cells derived from PDTALL46 PDX mice after an acute treatment with control Ab or OMP-52M51.

2023-09-13 | GSE224988 | GEO

Potential blood biomarkers for chronic traumatic encephalopathy: the multi-omics landscape of an observational cohort (serum exosomes miRNA microarray data)

Project description:Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts, which is susceptible in elderly people with declined mobility, athletes of full contact sports, military personnel and victims of domestic violence. It has been pathologically diagnosed in brain donors with a history of repetitive mild traumatic brain injury (rmTBI), but cannot be clinically diagnosed for a long time. By the continuous efforts by neuropathologists, neurologists and neuroscientists in recent 10 years, an expert consensus for the diagnostic framework of CTE was proposed in 2021 funded by the National Institute of Neurological Disorders and Stroke. The new consensus contributes to facilitating research in the field. However, it still needs to incorporate in-vivo biomarkers to further refine and validate the clinical diagnostic criteria. From this, a single-center, observational cohort study has been being conducted by Tianjin Medical University General Hospital since 2021. As a pilot study of this clinical trial, the present research recruited 4 pairs of gender- and age-matched rmTBI patients with healthy subjects. Their blood samples were collected for exosome isolation, and multi-omics screening to explore potential diagnostic biomarkers in blood and its exosomes.

2022-10-18 | E-MTAB-12329 | 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