Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [Bisulfite-Seq]

ABSTRACT: We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneous methylation of distal regulatory elements and transcriptional heterogeneity of key pluripotency genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE68642 | GEO | 2015/12/24

SECONDARY ACCESSION(S): PRJNA283282

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [RNA-seq]

2015-12-24 | GSE74534 | GEO

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [Bisulfite-Seq]

Project description:We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneous methylation of distal regulatory elements and transcriptional heterogeneity of key pluripotency genes. E14 ES cells were grown in either serum/LIF or 2i culture conditions and separated into single cells. RNA-Seq or Bisulfite-Seq libraries were prepared. This Series includes only the Bisulfite-Seq data. The list of 61 samples that passed QC in both BS-seq and RNA-seq is included in "Supplementary Table 1" of the associated manuscript.

2015-12-24 | E-GEOD-68642 | biostudies-arrayexpress

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity [RNA-seq]

Project description:We report scM&T-seq, a method for parallel single-cell genome-wide methylome and transcriptome sequencing, allowing discovery of associations between transcriptional and epigenetic variation. Profiling of 61 mouse embryonic stem cells confirmed known links between DNA methylation and transcription. Notably, the method reveals novel associations between heterogeneous methylation of distal regulatory elements and transcriptional heterogeneity of key pluripotency genes. E14 ES cells were grown in either serum/LIF or 2i culture conditions and separated into single cells. RNA-Seq or Bisulfite-Seq libraries were prepared. This Series includes only the RNA-Seq data. The list of 61 samples that passed QC in both BS-seq and RNA-seq is included in "Supplementary Table 1" of the associated manuscript.

2015-12-24 | E-GEOD-74534 | biostudies-arrayexpress

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq]

Project description:DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 *cis* methylation QTLs (meQTLs), i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs. Whole genomic DNA from 10 Yoruba HapMap individuals and spiked in unmethylated lambda phage DNA was bisuflite converted using the Invitrogen MethylCode Bisulfite Conversion Kit and sequenced using a Illumina HiSeq 2000

2014-05-09 | E-GEOD-57471 | biostudies-arrayexpress

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]

2014-05-09 | GSE57481 | GEO

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq]

2014-05-09 | GSE57471 | GEO

Sex comb on midleg (Scm) is a functional link between PcG repressive complexes in Drosophila

Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing

2015-07-09 | E-GEOD-66183 | biostudies-arrayexpress

Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]

Project description:DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified 11,752 methylation QTLs (meQTLs)—i.e., loci in which genetic variation is significantly associated with changes in DNA methylation. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNaseI accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest a shared and coordinated molecular variation in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that both changes in putative TF binding affinity and changes in the strength of TF binding footprints are associated with variation in DNA methylation near the TF binding sites. Considered together, our observations are consistent with a model whereby changes in TF binding may frequently drive coordinated changes in DNA methylation, histone modification, and gene expression levels. Bisulfite converted DNA from 64 individuals was hybridized to the Illumina Infinium HumanMethylation450 BeadChip

2014-05-09 | E-GEOD-57481 | biostudies-arrayexpress

Sex comb on midleg (Scm) is a functional link between PcG repressive complexes in Drosophila

2015-07-09 | GSE66183 | GEO

Parallel single-cell bisulfite- and RNA-sequencing link transcriptional and epigenetic heterogeneity

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-24 | E-GEOD-74535 | biostudies-arrayexpress