Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of retinae from wildtype and retinoschisin knockout mice (Rs1h-/Y) at postnatal day 7 to understand the effect of retinoschisin on gene expression

ABSTRACT: Genome-wide expression profiling of the retinoschisin deficient retina in C57CL/6 mice. Experiment Overall Design: RNAs from retinae from 3 Wildtype Mice versus 3 Retinoschisin-KO mice (Rs1h-/Y) at postnatal day 7 (P7) were hybridized onto Affymetrix microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Bernhard Weber

PROVIDER: E-GEOD-5581 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide expression profiling of the retinoschisin-deficient retina in early postnatal mouse development.

Gehrig Andrea A Langmann Thomas T Horling Franziska F Janssen Andreas A Bonin Michael M Walter Michael M Poths Sven S Weber Bernhard H F BH

Investigative ophthalmology & visual science 20070201 2

<h4>Purpose</h4>The Rs1h knockout mouse displays retinal features typical for X-linked juvenile retinoschisis (RS). Consequently, this mouse line represents an excellent model to study early molecular events in RS.<h4>Methods</h4>Whole genome expression profiling using DNA-microarrays was performed on total RNA extracts from retinoschisin-deficient and wild-type murine retinas from postnatal days 7, 9, 11, and 14. Quantitative real-time RT-PCR (qRT-PCR) analysis of additional time points facilit ...[more]

PMID: 17251492

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Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 mutations association with neurodevelopmental disorders such as ASD, ADHD, and intellectual disability, its role in physiological and pathological neurodevelopment is significantly unknown. Here, we use murine model to knockout Zmiz1 using Emx1Cre and performed RNA sequencing on P7 cortex to profile transcriptional changes upon Zmiz1 deletion. Timed pregnancy was carried out. Mice was euthanized using CO2 and embryos brain were extracted at E15.5. Cortex was dissected and dissociated into single cell suspension using Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628) following manufacture instruction. Intermediate progenitors were magnetically selected and isolated using Anti-Prominin-1 MicroBeads, mouse (Miltenyi Biotec, 130-092-333). Total RNA was extracted from wildtype and Zmiz1-KO samples. RNA concentration and RNA integrity number were determined. RNA library was prepared, quantified, and verified using TruSeq RNA Library Prep Kit v2, Qubit dsDNA High Sensitivity Assay kit and Bioanalyzer DNA1000 assay kit respectively. Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 on a Nextseq1000/2000. RNA-seq data analysis was performed using illumina BaseSpace Sequence Hub. Briefly, sequenced reads were aligned to mouse (mm10) reference genome with RNA-Seq alignment tool (STAR aligner) and differentially expressed genes (DEG) were determined using the RNA-Seq Differential Expression tool (version 1.0.1). Results: We found 114 differentially expressed genes of which 35 genes were upregulated while 69 genes were downregulated. Downregulated genes were enriched in biological processes such as forebrain deveopment, axon development, neuron differentiation etc. Conclusions: We assessed P7 cortex specific transcriptional profile changes which are potentially regulated by Zmiz1.

Dataset Information

Transcription profiling of retinae from wildtype and retinoschisin knockout mice (Rs1h-/Y) at postnatal day 7 to understand the effect of retinoschisin on gene expression

Publications

Genome-wide expression profiling of the retinoschisin-deficient retina in early postnatal mouse development.

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