Collateral Damage
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45713 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6064688.fastq.gz | Fastqsanger.gz | |||
| ERR6064688_1.fastq.gz | Fastqsanger.gz | |||
| ERR6064688_2.fastq.gz | Fastqsanger.gz | |||
| ERR6064689.fastq.gz | Fastqsanger.gz | |||
| ERR6064689_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY). In this dataset, we include probe-set level data obtained from vestibular macula samples. The processed data represent probe-set intensities that have been normalized to gene expression levels (Inorm). Inorm was calculated using batch-corrected data as well as data that were not corrected for a batch effect. 7 total samples were analyzed: vestibular maculas from 4 heterozygous (bv/+) and 3 homozygous (bv/bv) mouse embryos at E16.5.
2012-10-21 | E-GEOD-33590 | biostudies-arrayexpress
Project description:The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY). In this dataset, we include probe-set level data obtained from cerebellar samples. The processed data represent probe-set intensities that have been normalized to gene expression levels. 8 total samples were analyzed in this series: cerebellums from 4 heterozygous (bv/+) and 4 homozygous (bv/bv) mice at P15.
2012-10-21 | E-GEOD-33589 | biostudies-arrayexpress
Project description:The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY). In this dataset, we include probe-set level data obtained from vestibular macula samples. The processed data represent probe-set intensities that have been normalized to gene expression levels (Inorm). Inorm was calculated using batch-corrected data as well as data that were not corrected for a batch effect.
2012-10-21 | GSE33590 | GEO
Project description:The spontaneous mutant Bronx waltzer (bv) mouse line is characterized by deafness and balance defect. We located the bv mutation to the Srrm4 gene which encodes a regulator of alternative pre-mRNA splicing. We found that Srrm4 is expressed in balance and hearing organs (i.e. in the vestibular maculas and the cochlea). Srrm4 is also expressed in the central nervous system including the cerebellum. To identify potential splicing defects in bv/bv mice, we analyzed RNA samples from the vestibular maculas and cerebellums of bv/bv mice and control (bv/+) littermates, using mouse exon junction microarrays (MJAY). In this dataset, we include probe-set level data obtained from cerebellar samples. The processed data represent probe-set intensities that have been normalized to gene expression levels.
2012-10-21 | GSE33589 | GEO
Project description:Different mutations in the gene encoding humans IGF-I cause intrauterine growth retardation, postnatal growth failure, microcephaly, mental retardation, bilateral sensorineural deafness and multiple dysmorphic features. Insight into the role of IGFs in inner ear cochlear ganglion neurogenesis has come from the study of genetically modified mice. Postnatal cochlear development is severely impaired in mice Igf1-/-, which develop smaller cochlea and cochlear ganglia, an immature tectorial membrane and they display a significant decrease in the number and size of auditory neurons. We used microarrays to define the genetic signatures of Igf-1 +/+ and Igf-1-/- mouse cochea and identify the differentially expressed genes. Experiment Overall Design: Cochleae from two E18.5 were isolated from both Igf-1+/+ wild type and Igf-1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos 18.5 days post coitus (E18.5). Three independent pools were used. Cochlear tissues included the otic capsule but not vestibular tissues.
2008-10-21 | E-GEOD-11844 | biostudies-arrayexpress
Project description:Different mutations in the gene encoding humans IGF-I cause intrauterine growth retardation, postnatal growth failure, microcephaly, mental retardation, bilateral sensorineural deafness and multiple dysmorphic features. Insight into the role of IGFs in inner ear cochlear ganglion neurogenesis has come from the study of genetically modified mice. Postnatal cochlear development is severely impaired in mice Igf1-/-, which develop smaller cochlea and cochlear ganglia, an immature tectorial membrane and they display a significant decrease in the number and size of auditory neurons. We used microarrays to define the genetic signatures of Igf-1 +/+ and Igf-1-/- mouse cochea and identify the differentially expressed genes. Experiment Overall Design: Cochleae from two E18.5 were isolated from both Igf-1+/+ wild type and Igf-1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos 18.5 days post coitus (E18.5). Three independent pools were used. Cochlear tissues included the otic capsule but not vestibular tissues.
2009-02-10 | E-GEOD-11821 | biostudies-arrayexpress
Project description:Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the Qiagen® RNeasy® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChip® X. laevis Genome 2.0 Array. The OMIM database was mined for identification of genes causing deafness and vestibular disorder in humans. Human sequences for each of the deafness and vestibular disorders genes were downloaded from Ensembl. Blast-2.2.27+ was used to mapped the human sequences against X. tropicalis predicted proteins from JGI or to Xenopus consensus sequences downloaded from Affymetrix. The alignment of the human sequences to the predicted proteins resulted in the identification of the protein designation number. The protein designation number was used to obtain the sacaffold number and coordinates from JGI genome browser. The scaffold number and coordinates were input into Alpheus sequence variant detection pipeline to obtain the number of reads associated with each gene. The reads were log2 transformed for comparison to the microarray. In the case of the alignment of the human sequences to the Xenopus consensus sequences resulted in the PSID. The PSID was used to obtain the GCRMA intensity value. The GCRMA value and the number of reads were compared to determine which technology detected more genes. Results: Using Affymetrix GeneChip® X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies showed that RNA-Seq detected more of both deafness and vestibular disorder than the Microarray. RNA-Seq and microarray detected 108 genes but RNA-Seq detected 48 genes that were below threshold criteria for microarray. While the microarray detected 11 genes that were below the expression criteria for RNA-Seq and 23 genes were below the threshold criteria for both technologies. Further analysis of the 108 genes detected by both technologies showed a minor correlation between the two technologies. Conclusions: As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used for gene mutagenesis. Furthermore, results from this study showed that the two technologies can complement each other and that a combination of both approaches can provide a more complete analysis of gene expression than either method alone.
2016-02-28 | GSE69701 | GEO
Project description:The diminuendo mouse carries a mutation in the seed region of miR-96. Adult homozygotes are deaf and display vestibular defects, heterozygotes have rapidly progressive hearing loss. Microarray analysis of four day old homozygotes showed multiple transcripts were misregulated. Because the effect of the diminuendo mutation appears to be a retardation of development, we carried out this microarray on newborn homozygote and wildtype mice to examine the transcriptome at a younger age.
2016-02-26 | E-MTAB-3735 | biostudies-arrayexpress
Project description:Gene expression was analyzed in endolymphatic sacs of two groups of mice: Slc26a4Δ/Δ and Slc26a4Δ/+ mice. Slc26a4Δ/Δ mice fail to develop hearing and are a model for Enlarged Vestibular Aqueduct and Pendred Syndrome, two forms of human deafness that are associated with mutations of SLC26A4. Slc26a4Δ/+ mice develop normal hearing and served a controls. Gene expression was performed at embryonic day (E) 13.5, E14.5, E16.5 and E17.5, which are pathobiologically relevant time points that mark growth and enlargement of the entire inner ear including the cochlea and the vestibular aqueduct. Affymetrix microarrays were used to analyze gene expression and developmental changes in gene expression in Slc26a4Δ/Δ and Slc26a4Δ/+ mice with the goal to identify genes that are in a functional relationship with Slc26a4, the gene that codes for pendrin.
2017-09-22 | GSE90092 | GEO
Project description:Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis. Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the Qiagen® RNeasy® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChip® X. laevis Genome 2.0 Array. The OMIM database was mined for identification of genes causing deafness and vestibular disorder in humans. Human sequences for each of the deafness and vestibular disorders genes were downloaded from Ensembl. Blast-2.2.27+ was used to mapped the human sequences against X. tropicalis predicted proteins from JGI or to Xenopus consensus sequences downloaded from Affymetrix. The alignment of the human sequences to the predicted proteins resulted in the identification of the protein designation number. The protein designation number was used to obtain the sacaffold number and coordinates from JGI genome browser. The scaffold number and coordinates were input into Alpheus sequence variant detection pipeline to obtain the number of reads associated with each gene. The reads were log2 transformed for comparison to the microarray. In the case of the alignment of the human sequences to the Xenopus consensus sequences resulted in the PSID. The PSID was used to obtain the GCRMA intensity value. The GCRMA value and the number of reads were compared to determine which technology detected more genes. Results: Using Affymetrix GeneChip® X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies showed that RNA-Seq detected more of both deafness and vestibular disorder than the Microarray. RNA-Seq and microarray detected 108 genes but RNA-Seq detected 48 genes that were below threshold criteria for microarray. While the microarray detected 11 genes that were below the expression criteria for RNA-Seq and 23 genes were below the threshold criteria for both technologies. Further analysis of the 108 genes detected by both technologies showed a minor correlation between the two technologies. Conclusions: As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used for gene mutagenesis. Furthermore, results from this study showed that the two technologies can complement each other and that a combination of both approaches can provide a more complete analysis of gene expression than either method alone. Inner ear RNA from X. laevis larval stages 56-58 was isolated and shipped to the National Center for Genome Resources, for Illumina-Solexa sequencing or to the Massachusetts Institute of Technology BioMicro Center for microarray analysis with the Affymetrix GeneChip® X. laevis Genome 2.0 Array. RNA-Sequencing was completed using the Illumina-Solexa platform for sequencing by synthesis. Short-insert paired end (SIPE) libraries were prepared from total RNA according to Illuminaâ??s mRNA-Seq Sample Prep Protocol v2.0 (Illumina, San Diego, CA, USA). The resultant double-stranded cDNA concentration was measured on a NanoDrop spectrophotometer, and size and purity were determined on the 2100 Bioanalyzer using a DNA 1000 Nano kit. The cDNA libraries were cluster amplified on Illumina flowcells, sequenced on the GAII Sequencer as 36-cycle single-end reads, and processed using Illumina software v1.0. Illumina reads were aligned to the X. tropicalis genome using the algorithm for genomic mapping and alignment program (GMAP) and Alpheus® Sequence Variant Detection System v3.1.
2016-02-28 | E-GEOD-69701 | biostudies-arrayexpress