Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation data from ESCs derived by polar body transfer reconstructed embryos (PBTESCs)

ABSTRACT: Here we report the derivation of human ESCs from the polar body thansfer reconstructed embryos. We choose three cell lines from all the cell lines and compare the DNA methylation state. We use human methylation chip to compare genomic DNA methylation level among three PB1 transfer human ES cell lines and three PB2 transfer human ES cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE95761 | GEO | 2018/03/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Functional Haploid Human Oocytes Generated from Polar Body Genomes (RNA-Seq)

Project description:Oocyte defects lie at the heart of some forms of infertility and could potentially be addressed therapeutically by alternative routes for oocyte formation. Here, we describe the generation of functional human oocytes following nuclear transfer of first polar body (PB1) genomes from metaphase II (MII) oocytes into enucleated donor MII cytoplasm (PBNT). The reconstructed oocytes supported the formation of de novo meiotic spindles and, after fertilization with sperm, meiosis completion and formation of normal diploid zygotes. While PBNT zygotes developed to blastocysts less frequently (42%) than controls (75%), genome-wide genetic, epigenetic, and transcriptional analyses of PBNT and control ESCs indicated comparable numbers of structural variations and markedly similar DNA methylation and transcriptome profiles. We conclude that rescue of PB1 genetic material via introduction into donor cytoplasm may offer a source of oocytes for infertility treatment or mitochondrial replacement therapy for mtDNA disease.

2016-12-07 | GSE79309 | GEO

Functional Haploid Human Oocytes Generated from Polar Body Genomes (Bisulfite-Seq)

2016-12-07 | GSE79300 | GEO

mRNA expression data from ESCs derived by polar body transfer reconstructed embryos (PBTESCs)

Project description:Here we report the derivation of human PBTESCs from polar body transfer resconstructed embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES)、normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.

2018-03-04 | GSE95706 | GEO

Transcription profiling of human B cells at four cconsecutive stages of B cell development

Project description:Cells from four develppmental stages were purified by FACS from human bone marrow samples Experiment Overall Design: Cells were sorted as follows: PB1: CD34+VpreB+ PB2: VpreB-CD34+ LAR: kappa/lambda-VpreB-large SMA: kappa/lambda-VpreB-small. All cells were CD19+

2008-06-18 | E-GEOD-4590 | biostudies-arrayexpress

Detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.

Project description:Inherited mitochondrial DNA (mtDNA) diseases transmit maternally and cause severe phenotypes. Since no effective treatment or genetic screening is available, nuclear genome transfer between patients’ and healthy eggs to replace mutant mtDNAs holds promises. Since polar body contains very few mitochondria and share same genomic material as oocyte, here we perform polar body transfer to prevent the transmission of inherited mtDNA variants. We compare the value of different germline genome transfer (spindle-chromosome, pronuclear, first and second polar body) in a mouse model. Reconstructed embryos support normal fertilization and produce live offspring. Strikingly, genetic analysis confirms F1 generation after polar body transfer possesses minimal donor mtDNA carry-over compared with spindle-chromosome (low/medium carry-over) and pronuclear (medium/high carry-over) transfer. Moreover, mtDNA genotype remains stable in F2 generation of progeny after polar body transfer. Our preclinical model demonstrates polar body transfer holds great potential in preventing the transmission of inherited mtDNA diseases. The objective of the present study was to detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.

2014-06-19 | E-GEOD-56676 | biostudies-arrayexpress

ICL0011 - Host response in human Calu-3 cells to infection with A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB1-F2 deletion), A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB2-627E mutant) or WT: A/Vietnam/1203/2004 (H5N1)

2013-01-05 | GSE43203 | GEO

The second polar body contributes to the fate asymmetry in the mouse embryo

Project description:The second polar body (PB2) of mouse embryo may contains some crutial factors that control fate asymmetry. This study is aimed at discovering differentially expressed genes in PB2 compared with zygote.

2021-12-27 | GSE182918 | GEO

Project description:Differential expression was determined in Calu-3 cells between mock infected and infection with one of 3 Influenza viruses (wild-type VN1203, VN1203 mutant PB1-F2del, VN1203 mutant PB2-627E) at different times post infection. Purpose: To obtain samples for transcriptional analysis in triplicate using the VN1203 pathogenicity mutants PB1-F2del and PB2-627E. Overview of Experiment: . Time Points: 0, 3, 7, 12, 18 and 24 hrs post infection. . There are two time points for wild type VN1203. . Done in triplicate. . Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates. . Time-matched mocks were done in triplicate from the same cell stock as the rest of the samples. . Culture medium (the same as what the virus stock is in) was used for the mock infections. Calu-3 cells were infected with A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB1-F2 deletion), A/Vietnam/1203-CIP048_RG3/2004 (H5N1) (PB2-627E mutant) or mock infected and samples were collected at 0, 3, 7, 12, 18 and 24 hpi. Calu-3 cells were infected with WT: A/Vietnam/1203/2004 (H5N1) and samples were collected at 7 and 24 hpi. There are 3 mock and 3 infected replicates for each time point. Expression profiles were determined.

2013-01-05 | E-GEOD-43203 | biostudies-arrayexpress

The ubiquitin landscape of the Influenza A Virus polymerase

Project description:During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitin landscape of the IAV polymerase during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG- (di-glycyl)-remnant-bearing peptides. We identified 59 modified lysines across all three subunits of the viral polymerase of which 17 distinctively affected mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, our results demonstrate that the ubiquitinated residue K578 in the PB1 thumb domain is crucial for the dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R impeded the steps of cRNA stabilization and vRNA transcription, respectively, and affected NP binding as well as polymerase dimerization. Collectively, our results indicate that ubiquitin-mediated disruption of the charge-dependent interaction between PB1-K578 and PB2-E72 is required to coordinate polymerase dimerization and facilitate vRNA replication, which demonstrates that IAV exploit the cellular ubiquitin system to modulate the activity of the viral polymerase for the regulation of viral replication.

2023-03-11 | PXD030816 | Pride

DNA methylation programming and reprogramming in primate embryonic stem cells

Project description:DNA methylation is an important epigenetic mechanism, affecting normal development and playing a key role in reprogramming epigenomes during stem cell derivation. Here we report on DNA methylation patterns in native monkey embryonic stem (ES) cells, fibroblasts and ES cells generated through somatic cell nuclear transfer (SCNT), identifying and comparing epigenome programming and reprogramming. We characterize hundreds of regions that are hyper- or hypo- methylated in fibroblasts compared to native ES cells and show that these are conserved in human cells and tissues. Remarkably, the vast majority of these regions are reprogrammed in SCNT ES cells, leading to almost perfect correlation between the epigenomic profiles of the native and reprogrammed lines. At least 58% of these changes are correlated in cis to transcription changes, Polycomb Repressive Complex-2 occupancy, or binding by the CTCF insulator. We also show that while epigenomic reprogramming is extensive and globally accurate, the efficiency of adding and stripping DNA methylation during reprogramming is regionally variable. In several cases, this variability results in regions that remain methylated in a fibroblast-like pattern even after reprogramming. DNA methylation profiles in rhesus monkey native ES cells (ORMES-22), fibroblasts, and ES cells generated by somatic cell nuclear transfer (CRES-2), as well as a distinctly different native ES line (the homozygous parthenote ORMES-9) to control for ES line specific effects were identified via hybridization to a custom array including a set of human ESC bivalent domains combined with additional methylation related domains and control regions.

2009-09-10 | E-GEOD-17981 | 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