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| Status |
Public on Apr 17, 2018 |
| Title |
Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific, and brain region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.
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| Overall design |
We performed RNA-Seq on retina, motor cortex, SCN and visual cortex from normal- and dark-reard mouse and DNA-Seq on one mouse tail. The strain of mouse is a hybrid of B6 and CAST. F1i is the offspring from the mating of female CAST and male B6 mice. The F1r is the offspring from the mating of female B6 and male CAST mice.
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| Contributor(s) |
Huang H |
| Citation(s) |
29346572 |
| |
| Submission date |
Apr 24, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Hsien-Sung Huang |
| E-mail(s) |
huang.hsiensung@gmail.com
|
| Organization name |
National Taiwan University
|
| Street address |
Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.
|
| City |
Taipei |
| ZIP/Postal code |
10051 |
| Country |
Taiwan |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA384021 |
| SRA |
SRP105081 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98117_103251_103407_ASE_FOR_REV.xlsx |
67.2 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103251_103407_gene_expression.xlsx |
4.1 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103251_103407_isoform_expression.xlsx |
12.8 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103821_1223_ASE.xlsx |
61.5 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103821_1223_gene.xlsx |
5.6 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103821_1223_isoform.xlsx |
14.4 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103888_1230_gene.xlsx |
5.6 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103888_1230_isoform.xlsx |
15.4 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103888_retina_SCN_ASE.xlsx |
58.7 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103961_retina_SCN_ASE103961.xlsx |
61.6 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103961_retina_SCN_gene.xlsx |
5.6 Mb |
(ftp)(http) |
XLSX |
| GSE98117_103961_retina_SCN_isoform.xlsx |
15.6 Mb |
(ftp)(http) |
XLSX |
| GSE98117_RAW.tar |
494.8 Mb |
(http)(custom) |
TAR (of XLSX) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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