Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of Dnmt3L heterozygous and wildtype spermatocytes and spermatids

ABSTRACT: Comparison of gene expression differences between Dnmt3L heterozygous and wildtype pachytene spermatocytes, and similarly between Dnmt3L heterozygous and wildtype round spermatids which were isolated from the Dnmt3L knockout mouse line. This array was conducted to address the hypothesis that Dnmt3L heterozygosity results in deregulated gene expression within spermatocytes and spermatids. Results show that Dnmt3L heterozygosity causes numerous genes to be differentially regulated on a genome-wide level, showing that DNMT3L has an important role in regulating gene expression within these male germ cells. Three preparations each of Dnmt3L purified wildtype spermatocytes, wildtype spermatids, heterozygous spermatids, and two preparations of heterozygous spermatocytes were isolated for a total of 11 samples. Each preparation was made up of cells isolated from 10 mice.

ORGANISM(S): Mus musculus

SUBMITTER: Gordon Smyth

PROVIDER: E-GEOD-20241 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide analysis of Dnmt3L heterozygous and wildtype spermatocytes and spermatids

Project description:Comparison of gene expression differences between Dnmt3L heterozygous and wildtype pachytene spermatocytes, and similarly between Dnmt3L heterozygous and wildtype round spermatids which were isolated from the Dnmt3L knockout mouse line. This array was conducted to address the hypothesis that Dnmt3L heterozygosity results in deregulated gene expression within spermatocytes and spermatids. Results show that Dnmt3L heterozygosity causes numerous genes to be differentially regulated on a genome-wide level, showing that DNMT3L has an important role in regulating gene expression within these male germ cells.

2011-03-01 | GSE20241 | GEO

Mus musculus

Project description:Genome-wide analysis of Dnmt3L heterozygous and wildtype spermatocytes and spermatids

| PRJNA125745 | ENA

Dnmt3l-/+ (maternal methylation-deficient) vs normal 8.5dpc embryos

Project description:During oogenesis, DNA methyltransferase 3-like (Dnmt3l) is required for the establishment of the maternal germline DNA methylation imprints that in the offspring, govern the parent-of-origin-specific expression of most known imprinted genes (Science 2001, 294:2536-9). Dnmt3l-deficient dams were crossed with wildtype sires to obtain Dnmt3l-/+ embryos that lack maternal methylation imprints. Gene expression was measured in Dnmt3l-/+ and wildtype embryos and is expected to differ for imprinted genes that are under the control of a maternal methylation mark. Keywords: genetic modification, DNA methylation

2008-04-14 | GSE8756 | GEO

Transcription profiling of mpuse Dnmt3l-/+ (maternal methylation-deficient) vs normal 8.5dpc embryos

2008-06-16 | E-GEOD-8756 | biostudies-arrayexpress

Transcription profiling of mouse Dnmt3L+/- sires compared to offspring of Dnmt3L+/+ sires to investigate the effect of paternal haploinsufficiency for Dnmt3L

Project description:There is increasing evidence that epigenetic information can be inherited across generations in mammals, despite extensive reprogramming both in the gametes and the early developing embryo. One corollary to this is that disruption of the establishment of epigenetic state in the gametes of a parent, as a result of heterozygosity for mutations in genes involved in reprogramming, could affect the phenotype of offspring that do not inherit the mutant allele. Here we show that such effects do occur following paternal inheritance in the mouse. We detect changes to transcription and chromosome ploidy in adult animals. Paternal effects of this type have not been reported previously in mammals and suggest that the untransmitted genotype of male parents can influence the phenotype of their offspring. Experiment Overall Design: Offspring of Dnmt3L+/- sires compared to offspring of Dnmt3L+/+ sires

2008-06-15 | E-GEOD-7384 | biostudies-arrayexpress

The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids

Project description:Background: The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin modifications and their effects on global gene expression patterns, in spermatocytes and spermatids. Results: HR6B is enriched on the XY body and on centromeric regions in pachytene spermatocytes. Global gene expression analyses revealed that spermatid-specific single- and multicopy X-linked genes are prematurely expressed in Hr6b knockout spermatocytes. Very few other differences in gene expression were observed in these cells, except for upregulation of major satellite repeat transcription. In contrast, in Hr6b knockout spermatids, 7298 genes were differentially expressed; 65% of these genes was downregulated, but we observed a global upregulation of gene transcription from the X chromosome. In wildtype spermatids, approximately 20% of the single-copy X-linked genes reach an average expression level that is similar to the average expression from autosomes. Conclusions: Spermatids maintain an enrichment of repressive chromatin marks on the X chromosome, originating from meiotic prophase, but this does not interfere with transcription of the single-copy X-linked genes that are reactivated or specifically activated in spermatids. HR6B represses major satellite repeat transcription in spermatocytes, and functions in the maintenance of X chromosome silencing in spermatocytes and spermatids. It is discussed that these functions involve modification of chromatin structure, possibly including H2B ubiquitylation. 8 Affymetrix microarrays were generated: 4 from wildtype and HR6B knockout spermatocytes (2 replicates each), and 4 from wildtype and HR6B knockout spermatids (2 replicates each).

2010-05-27 | E-GEOD-21749 | biostudies-arrayexpress

The effect of paternal haploinsufficiency for Dnmt3L

Project description:There is increasing evidence that epigenetic information can be inherited across generations in mammals, despite extensive reprogramming both in the gametes and the early developing embryo. One corollary to this is that disruption of the establishment of epigenetic state in the gametes of a parent, as a result of heterozygosity for mutations in genes involved in reprogramming, could affect the phenotype of offspring that do not inherit the mutant allele. Here we show that such effects do occur following paternal inheritance in the mouse. We detect changes to transcription and chromosome ploidy in adult animals. Paternal effects of this type have not been reported previously in mammals and suggest that the untransmitted genotype of male parents can influence the phenotype of their offspring. Keywords: Offspring of Dnmt3L+/- sires compared to offspring of Dnmt3L+/+ sires

2007-03-29 | GSE7384 | GEO

Expression profiling of isolated populations of prepachytene spermatocytes, pachytene spermatocytes and spermatids of PWD and B6 males

Project description:Expression profiling of isolated populations of prepachytene spermatocytes (LP), pachytene spermatocytes (RP) and spermatids (ST) from PWD and B6 was performed to study the genome wide variation in gene expression between two mouse subspecies. To evaluate the transcriptional difference between B6 and PWD in during meiosis, we compared their transcriptomes in sorted populations of pre-pachytene primary spermatocytes (Leptonema, Zygotene and Pachytene), pachytene spermatocytes (Mid-late pachytene and diplotene) and spermatids. Populations of pre-pachytene spermatocytes, pachytene spermatocytes and spermatids were isolated from PWD and B6 mice. All populations were isolated in duplicates from two animals. Hence, RNA was prepared from 12 samples (= 2 strains x 3 tissues x 2 replicas) and was then subject to labeling and hybridization on microarray chips.

2014-06-01 | E-GEOD-49444 | biostudies-arrayexpress

TMT-based proteomics analysis of mouse germ cells

Project description:The proteome changes were quantified in RibosomeRPL39L-/- spermatocytes and elongated spermatids using TMT 6-plex, and in spermatogonia, spermatocytes, round spermatids and elongated spermatids using TMT 10-plex by LC-MS/MS.

2022-10-05 | PXD020874 | Pride

Expression profiling of isolated populations of prepachytene spermatocytes, pachytene spermatocytes and spermatids of PWD and B6 males

2014-06-01 | GSE49444 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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