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Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

ABSTRACT: We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes.

ORGANISM(S): Mus musculus Lambdavirus lambda

PROVIDER: GSE47343 | GEO | 2013/08/31

SECONDARY ACCESSION(S): PRJNA205186

REPOSITORIES: GEO

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Single cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing

Project description:We develop a single cell methylome analysis technique based on RRBS, which works robustly for mouse embryonic stem cells (mESCs), sperm, metaphase II oocytes, and zygotes. In total, 36 samples were analyzed, including 8 single mouse embryonic stem cells (mESCs), pooled-5, 10, 20 mESCs, bulk mESCs, 7 single sperms, 10 single pronuclei from 5 individual zygotes, 2 metaphase II oocytes, 2 the first polar bodies and 3 negative controls.

2013-08-31 | E-GEOD-47343 | biostudies-arrayexpress

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.

Project description: Not available

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RRBS (Reduced Representation Bisulfite Sequencing) of HL60

Project description:We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). Genes were then stratified by the expression profile ultimately leading to the epitranscriptome map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

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RRBS (Reduced Representation Bisulfite Sequencing) of HL60

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Reduced representation bisulfite sequencing data of mouse genome

Project description:RRBS was used to analyse global imprinting gene methylation pattern of offspring from the in vitro derived spermatids like cells and normal control

2016-02-26 | GSE76238 | GEO

Quantitative reduced representation bisulfite sequencing with unique molecular identifiers of single cell

Project description:Reduced representation bisulfite sequencing (RRBS) has been proven a powerful method in DNA methylome profiling. Since the initial development of this method, the RRBS protocol has been modified in order to optimize it for genomic coverage, starting material, and library-construction throughput, which has resulted in new methods such as enhanced RRBS (ERRBS), double-enzyme RRBS (dRRBS), gel-free and multiplexed RRBS (mRRBS), and single-cell RRBS (scRRBS). However, each of these methods has failed to address PCR-derived duplication artifacts, which can bias the results of DNA methylation analyses. To overcome the aforementioned complication, we developed quantitative RRBS (Q-RRBS), a method in which unique molecular identifiers (UMIs) are used to eliminate PCR-induced duplication. By performing Q-RRBS on varying amounts of starting material, we determined that duplication-induced artifacts were more severe when small quantities of the starting material were used. However, through using the UMIs, we successfully eliminated these artifacts. Our results demonstrate that Q-RRBS is an optimal strategy for DNA methylation profiling of single cells or samples containing ultra-trace amounts of cells.

2016-01-14 | GSE76863 | GEO

Reduced representation bisulfite sequencing of equine tissue

Project description:The aim of the project was to identify the tissue-specific DNA methylation patterns of selected horse tissues, derived from two germ layers, endodermal (liver and lung) and mesenchymal (cardiac striated muscle) origin. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique.

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Reduced representation bisulfite sequencing data of mouse genome

Project description:RRBS was used to analyse global imprinting gene methylation pattern of offspring from the in vitro derived spermatids like cells and normal control Global imprinting gene methylation pattern comparision of two offspring (one male and one female) from the in vitro derived spermatids like cells and two normal control mice (one male and one female)

2016-02-26 | E-GEOD-76238 | biostudies-arrayexpress

Reduced Representation Bisulfite Sequencing from HD knock-in mouse model

Project description:We generated two types of DNA methylation datasets (Reduced Representation Bisulfite Sequencing [RRBS] and custom methylation array) from a heterozygous HD knock-in mouse model. The heterozygous Htt knock-in line expressed one wildtype endogenous Htt allele and a second Htt allele with knock-in of human mHTT exon 1 with either approximately 190 CAG repeats (Q175) or 20 CAG repeats (Q20). For each genotype (Q175 and Q20) we analyzed two brain regions (striatum and cerebellum) from 8 mice each on the RRBS platform (N=32 RRBS samples). Our EWAS of mutant Htt gene status (i.e. Q175 status) across the two brain regions identified two genome-wide significant CpGs in Htt region. contributor: CHDI foundation

2020-07-02 | GSE147156 | GEO

Reduced representation bisulfite sequencing (RRBS) of haploid, diploid and triploid hESCs

Project description:To test the differences in genome-wide DNA methylation signatures of haploid, diploid and triploid hESCs, we extracted genomic DNA from these cells and performed RRBS.

2023-05-04 | E-MTAB-11478 | biostudies-arrayexpress

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