Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A survey of imprinted gene expression in mouse trophoblast stem cells

ABSTRACT: Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had previously been described as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. Several genes showed variability in imprinted expression between the six TSC lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs, and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across a panel of six TSC lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for eight genes examined in all six independently derived TSC lines. Our results solidify TSCs as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse. RNA-Seq from F1 hybrid TSC lines generated from crosses between Cast and B6 mice.

ORGANISM(S): Mus musculus

SUBMITTER: J Calabrese

PROVIDER: E-GEOD-63968 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Defining principles of gene and regulatory element imprinting in mouse trophoblast stem cells

Project description:An undefined number of mammalian genes are expressed preferentially from one parental allele, in a process termed genomic imprinting. To shed light on the general principles of this process in a single cell type, we profiled allelic gene expression, DNaseI hypersensitivity (DHS), and CTCF binding in genetically defined murine trophoblast stem cells (TSCs). The data deposited in this entry are from CTCF ChIP-Seq and DNase-Seq experiments performed in the BC.1 cell line. All other data has been previously deposited as part of GEO Series GSE39406. The F1 TSC line profiled was generated from a cross between a C57BL/6J (B6) female and CAST/EiJ (Cast) male mouse.

2016-07-03 | E-GEOD-51610 | biostudies-arrayexpress

Site-specific silencing of regulatory elements as a mechanism of X-inactivation

Project description:The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequence is unknown. This study reports the profiling of Xi gene expression and chromatin states at high-resolution via allele-specific sequencing in F1 hybrid mouse trophoblast stem cells (TSCs). Datasets provided include those generated from strand-specific RNA-Seq, ChIP-Seq, FAIRE-Seq, and DNase-Seq protocols. Included for each dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads. The F1 TSC lines profiled were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice. C/B denotes a Cast mother and B6 father, and B/C denotes a B6 mother and Cast father.

2012-11-21 | E-GEOD-39406 | biostudies-arrayexpress

A survey of imprinted gene expression in mouse trophoblast stem cells

Project description:Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had previously been described as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. Several genes showed variability in imprinted expression between the six TSC lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs, and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across a panel of six TSC lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for eight genes examined in all six independently derived TSC lines. Our results solidify TSCs as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.

2015-02-24 | GSE63968 | GEO

CTCF binding patterns in mouse trophoblast stem cells

Project description:This Series reports data from a CTCF ChIP-Seq experiment performed in F1-hybrid mouse trophoblast stem cells (TSCs). The data are part of a larger study examining inactive X gene expression and chromatin states, reported as GEO Series GSE39406. Included for this dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads Single CTCF ChIP-Seq experiment

2012-09-08 | E-GEOD-40667 | biostudies-arrayexpress

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Project description:Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Examination of parent-of-origin specific and total gene expression in embryo, endosperm, and whole seeds. Samples with the same heading are biological replicates (e.g. CVN1, CVN2, and CVN3). High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col, Ler and Cvi reciprocal F1 hybrid embryo and endosperm tissue isolated at 6 days after pollination to identify imprinted genes.

2014-07-08 | E-GEOD-52806 | biostudies-arrayexpress

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

Project description:Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Sequencing of 12 small RNA samples from whole seeds 6 days after pollination.

2014-07-08 | E-GEOD-52807 | biostudies-arrayexpress

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [MeDIP-seq]

Project description:Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both “tetra-on” and corresponding “tetra-off” iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells Examination of DNA methylation in 13 cell types

2013-12-06 | E-GEOD-36293 | biostudies-arrayexpress

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [sRNA-seq]

2013-12-06 | E-GEOD-36291 | biostudies-arrayexpress

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq]

Project description:Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. Therefore, it becomes indispensable to exploit other reliable molecular markers for evaluating the quality of iPS cells accurately. In the present study, we successfully utilize the sequential reprogramming approach and produce all-iPS mice to six generations using iPS cell lines derived from different cell lineages which contain the same proviral integration in the genome. By comparing the global gene expression and epigenetic modifications of both "tetra-on" and corresponding "tetra-off" iPS cell lines established from either mesenchymal or hematopoietic lineages through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4m2, H3K4me3 and H3K27me3) and DNA methylation, very few differences are detected among all the iPS cell lines investigated. However, we find that two imprinted genes, disruption of which correlate with the reduced pluripotency of iPS cells. Therefore, our data not only provide the first demonstration that producing of all-iPS mice to six generations is feasible, but reveal that two imprinted regions can be served as pluripotency markers of iPS cells. Examination of the mRNA expression in 13 cell types

2013-12-06 | E-GEOD-36290 | biostudies-arrayexpress

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [ChIP-seq]

2013-12-06 | E-GEOD-36292 | biostudies-arrayexpress

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