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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole Genome Bisulfite Sequencing (WGBS) of cKIT+ sorted cells from 57-137 day old fetal testes and ovaries.

ABSTRACT: We performed WGBS analyses on 6 human fetal samples at 53-137 days of development, 4 female and 2 male. We show that methylation reprogramming in the human germline is global yet incomplete with exons, 3’UTRs and human-specific transposons remaining methylated. Whole Genome Bisulfite-Seq of cKIT+ cells analyzed from 4 biological samples for fetal ovaries from 57-113 days of development and 2 samples for fetal testes at 59 and 137 days of development.

ORGANISM(S): Homo sapiens

SUBMITTER: Sofia Gkountela

PROVIDER: E-GEOD-63393 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA Demethylation Dynamics in the Human Prenatal Germline.

Gkountela Sofia S Zhang Kelvin X KX Shafiq Tiasha A TA Liao Wen-Wei WW Hargan-Calvopiña Joseph J Chen Pao-Yang PY Clark Amander T AT

Cell 20150521 6

Global DNA demethylation in humans is a fundamental process that occurs in pre-implantation embryos and reversion to naive ground state pluripotent stem cells (PSCs). However, the extent of DNA methylation reprogramming in human germline cells is unknown. Here, we performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germline is distinct from ...[more]

PMID: 26004067

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cKIT+ sorted cells from 57-137 day old fetal testes and ovaries

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2015-05-28 | E-GEOD-63394 | biostudies-arrayexpress

Length-dependent gene misregulation in Rett syndrome (Bisulfite-seq)

Project description:Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with features of autism. MECP2 encodes a methyl-DNA-binding protein that is proposed to function as a transcriptional repressor, but, despite numerous studies examining neuronal gene expression in MeCP2 mutants, no coherent model has emerged for how MeCP2 regulates transcription. Here we identify a genome-wide length-dependent increase in the expression of long genes in neurons lacking MeCP2. This gene misregulation occurs in human RTT brains and correlates with onset and severity of phenotypes in Mecp2 mutant mice, suggesting that the disruption of long gene expression contributes to RTT pathology. We present evidence that MeCP2 represses long genes by binding to brain-enriched, methylated CA dinucleotides within genes and show that loss of methylated CA in the brain recapitulates gene expression defects observed in MeCP2 mutants. We find that long genes encode proteins with neuronal functions, and overlap substantially with genes that have been implicated in autism and Fragile X syndrome. Reversing the overexpression of long genes in neurons lacking MeCP2 can improve some RTT-associated cellular deficits. These findings suggest that a function of MeCP2 in the mammalian brain is to temper the expression of genes in a length-dependent manner, and that mutations in MeCP2 and possibly other autism genes may cause neurological dysfunction by disrupting the expression of long genes in the brain. Bisulfite-seq from mouse cortex and cerebellum

2015-03-12 | E-GEOD-60062 | biostudies-arrayexpress

RNA-Seq of cKIT+ sorted cells from 53-137 day old fetal testes and ovaries and RNA-Seq of TRA-1-81+ H1 and UCLA1 hESCs.

Project description:We performed RNA-Seq analyses on 15 human fetal samples at 53-137 days of development, 9 female and 5 male, and identified the transcriptional changes during the transition of human cKIT+ primordial germ cells (PGCs), the precursors of gametes, to the generation of Advanced Germline Cells. Comparing the transcriptional profile of PGCs to that of H1 and UCLA1 hESCs identifies differences between the two cell types and pinpoints molecules that can be used in the development of in vitro germ cell differentiation protocols starting from human pluripotent stem cells. RNA-Seq of cKIT+ cells analyzed from 6 biological samples for testes and 9 samples for ovaries from 53-137 days. 2 biological replicates of TRA-1-81+ cells sorted from H1 and UCLA1 hESCs. WGBS of cKIT+ cells analyzed from 4 biological samples of ovaries and 1 biological sample of testes at 57-137 days of development.

2015-05-28 | E-GEOD-63392 | biostudies-arrayexpress

Reduced representation bisulfite sequencing of liver DNA of 4-week old Bhmt-null mice (N=8) and wild type controls (N=8)

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2015-01-01 | E-GEOD-56359 | biostudies-arrayexpress

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

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2015-01-20 | E-GEOD-56429 | biostudies-arrayexpress

Frequent and Transient Acquisition of Pluripotency During Somatic Cell Trans-Differentiation with iPSCs Reprogramming Factors (WGBS)

Project description:Recent reports have proposed a new paradigm for obtaining mature somatic cell types from fibroblasts without going through a pluripotent state, by briefly expressing canonical iPSC reprogramming factors Oct4, Sox2, Klf4 and c-Myc (abbreviated as OSKM), in cells expanded in lineage differentiation promoting conditions. Here we apply genetic lineage tracing for endogenous Nanog, Oct4 and X chromosome reactivation during OSKM induced trans-differentiation, as these molecular events mark final stages for acquisition of induced pluripotency. Remarkably, the vast majority of reprogrammed cardiomyocytes or neural stem cells derived from mouse fibroblasts via OSKM mediated trans-differentiation were attained after transient acquisition of pluripotency, and followed by rapid differentiation. Our findings underscore a molecular and functional coupling between inducing pluripotency and obtaining “trans-differentiated” somatic cells via OSKM induction, and have implications on defining molecular trajectories assumed during different cell reprogramming methods. WGBS (Whole-Genome-Bisulfite-sequencing) were measured during conversion of mouse embryonic fibroblasts to neural stem cells using OSKM trans-differentiation method, as well as in mouse emrbyonic fibroblasts, and mouse ESCs.

2015-05-07 | E-GEOD-68601 | biostudies-arrayexpress

Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain

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