Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens
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ABSTRACT:
PROVIDER: PRJNA882908 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21666269.fastq.gz | Fastqsanger.gz | |||
| SRR21666270.fastq.gz | Fastqsanger.gz | |||
| SRR21666271.fastq.gz | Fastqsanger.gz | |||
| SRR21666272.fastq.gz | Fastqsanger.gz | |||
| SRR21666273.fastq.gz | Fastqsanger.gz |
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Project description:Using whole genome bisulfite sequencing (WGBS), we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5) using microdissected lenses. Histone H3.3 variant chromatin landscapes were also generated by ChIP-seq using microdissected newborn lenses.
2022-09-24 | GSE213901 | GEO
Project description:Foxp1 was strongly expressed in developing lens, and its knockout in lens resulted in failure of appropriate lens development. By microarray analysis, we examined effects of loss-of Foxp1 for gene expression pattern of lens at P0 developmental stage.
2018-01-17 | GSE93693 | GEO
Project description:Purpose: Transcriptome is the entire repertoire of all transcripts present in a cell at any particular time. We undertook next-generation whole transcriptome sequencing approach to gain insight of the transcriptional landscape of the developing mouse lens. Methods: We ascertained mice lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. Results: Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens. Of these, 46 genes exhibited 40-fold differential expression compared to transcriptional levels at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens. Of these, 49 miRNAs manifested an 8-fold or higher differential expression when compared, as above to the microRNA expression at E15. Conclusion: We report the first comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for development of the ocular lens and maintenance its transparency. Whole transcrtiome and microRNA profilling of mouse lens using 2 embryonic (E15 and E18) and 4 postnatal stages (P0, P3, P6 and P9) in duplicates through high-throughput sequening using Illumina HiSeq2000.
2015-10-29 | E-GEOD-69221 | biostudies-arrayexpress
Project description:The proteome is a term used for the entire catalog of proteins present in a cell at any time. In here, we investigated the proteome of developing mouse lens through mass spectrometry-based protein sequencing. We extracted mouse lenses at six developmental time points, which included two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The lenses from each time point were preserved in three distinct pools to serve as biological replicates for each developmental stage. The total cellular protein was extracted from the lens, digested with trypsin and labeled with 6-plex isobaric tandem mass tags (TMT) for three independent 6-plex TMT experiments. A total of 6,117 proteins were identified in the mouse ocular lens in at least one of the above-mentioned six developmental time points. Of these, 6,117 proteins were present in one TMT set, 4,325 in two, and 2,972 were present in three TMT sets, respectively. Majority of the proteins exhibit steady expression; however, we identified 162 proteins that exhibited an 8-fold differential (higher or lower) expression during the developmental time course compared to their levels at E15. The lens proteome is comprised of diverse proteins that have distinct biological properties and functional characteristics including a total of 404 proteins that have been associated with autophagy. We have established a comprehensive profile of the developing murine lens proteome. This repository will be helpful in identifying critical components of lens development and processes essential for the maintenance of its transparency.
2018-01-22 | PXD006381 | Pride
Project description:Purpose: Transcriptome is the entire repertoire of all transcripts present in a cell at any particular time. We undertook next-generation whole transcriptome sequencing approach to gain insight of the transcriptional landscape of the developing mouse lens. Methods: We ascertained mice lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. Results: Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens. Of these, 46 genes exhibited 40-fold differential expression compared to transcriptional levels at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens. Of these, 49 miRNAs manifested an 8-fold or higher differential expression when compared, as above to the microRNA expression at E15. Conclusion: We report the first comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for development of the ocular lens and maintenance its transparency.
2015-10-29 | GSE69221 | GEO
Project description:Methylation at cytosines (mCG) is a well-known regulator of gene expression but its requirements for cellular differentiation have yet to be fully elucidated. A well-studied cellular differentiation model system is the eye lens, consisting of a single anterior layer of epithelial cells that migrate laterally and differentiate into a core of fiber cells. Here, we explore the genome-wide relationships between mCG methylation, chromatin accessibility and gene expression during differentiation of eye lens epithelial cells into fiber cells. Whole genome bisulfite sequencing identified 7621 genomic loci exhibiting significant differences in mCG levels between lens epithelial and fiber cells. Changes in mCG levels were inversely correlated with the differentiation state-specific expression of 1285 genes preferentially expressed in either lens fiber or lens epithelial cells (Pearson correlation r = -0.37, p < 1x10-42). mCG levels were inversely correlated with chromatin accessibility determined by Assay for transposase-accessible sequencing (ATAC-seq) (Pearson correlation r = -0.86, p < 1x10-300). Many of the genes exhibiting altered regions of DNA methylation, chromatin accessibility and gene expression levels in fiber cells relative to epithelial cells are associated with lens fiber cell structure, homeostasis and transparency. These include lens crystallins (CRYBA4, CRYBB1, CRYGN, CRYBB2), lens beaded filament proteins (BFSP1, BFSP2), transcription factors (HSF4, SOX2, HIF1A), and Notch signaling pathway members (NOTCH1, NOTCH2, HEY1, HES5). Analysis of regions exhibiting cell-type specific alterations in DNA methylation revealed an overrepresentation of consensus sequences of multiple transcription factors known to play key roles in lens cell differentiation including HIF1A, SOX2, and the MAF family of transcription factors. Collectively, these results link DNA methylation with control of chromatin accessibility and gene expression changes required for eye lens differentiation. The results also point to a role for DNA methylation in the regulation of transcription factors previously identified to be important for lens cell differentiation.
2022-03-31 | GSE196629 | GEO
Project description:Microarray analysis comparing the gene expression of three tissues laser-microdissected from 1-month-old lenses in mice. The original study aimed to discover additional genes that belong to a distinct subset caled late fiber genes which are expressed in cells bordering the organelle-free-zone (OFZ) of the lens.
2022-06-03 | GSE205379 | GEO
Project description:Identification of genes involved in ocular birth defects remains a challenge. To facilitate the identification of genes associated with cataract, we developed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE contains microarray gene expression profiles of the mouse embryonic lens as it transitions from the stage of placode invagination to that of vesicle formation. We identified differentially regulated genes by comparing lens microarray profiles to those representing whole embryonic body (WB) without ocular tissue. These were then utilized to generate a ranked list of lens-genes enrichment, which can be viewed as iSyTE tracks in the UCSC Genome browser to aid identification of genes with lens function. We microdissected embryonic lens from mice at E10.5, E11.5, and E12.5 (triplicate at each time point). To have a proper control, we also generated gene expression profiles of whole embryonic body (WB) at these time points. For comparative analysis, we also generated gene expression profiles of E13.5 tooth germs tissues, and matched WB. These profiles are used to identify lens and tooth specific gene expression enrichment at these embryonic time points. This dataset is then used to prioritize analysis of candidate cataract associated genes.
2012-02-16 | E-GEOD-32334 | biostudies-arrayexpress
Project description:The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that require a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens. The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency. These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination. Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens. Our analysis detected over 15,000 unique transcripts expressed by the embryonic chicken lens. Of these, over 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells. Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination. These included differences in the expression levels of metabolic, autophagy, and mitophagy transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells. Differentiation-state transcriptional analysis of embryonic chicken lenses was performed following microdissection of 100 embryonic day 13 (E13) chicken lenses into four distinct regions that represent a continuum of lens cell differentiation states: lens central epithelium (EC), equatorial epithelium (EQ), cortical fibers (FP), and central fibers (FC). Further analysis of the transcriptional content of biologically replicate samples was performed by Illumina directional mRNA sequencing and resulting reads mapped by TopHat and assembled with Cufflinks.
2014-07-02 | E-GEOD-53976 | biostudies-arrayexpress
Project description:We performed ATAC-seq for microdissected lens epithelium and fiber from E14.5 and P0.5 mouse lenses.Through investigating dynamics of chromatin changes during mouse lens fiber and epithelium differentiation, we identified spatial-temporal differential accessible regions and the enriched known and novel motifs. We also discovered some novel and known enhancers for the transcription factors and structural genes that are important in lens development. Additionally, a cross examination of Pax6 ChIP-seq with ATAC-seq data revealed novel Pax6 binding mechanisms.
2019-05-13 | GSE124497 | GEO