Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE137744 | GEO | 2020/07/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing.

Project description:We have adapted transposase-based in vitro shotgun library construction ("tagmentation") for whole-genome bisulfite sequencing. This method, Tn5mC-seq, enables a >100-fold reduction in starting material relative to conventional protocols, such that we generate highly complex bisulfite sequencing libraries from as little as 10 ng of input DNA, and ample useful sequences from 1 ng of input DNA. We demonstrate Tn5mC-seq by sequencing the methylome of a human lymphoblastoid cell line to ?8.6× high-quality coverage of each strand.

| S-EPMC3371708 | biostudies-literature

Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

Project description:We applied whole genome bisulfite Sequencing data and profiled genome-wide DNA methylation distribution in four germ cell types during spermatogenesis.

2020-07-17 | GSE137743 | GEO

ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

Project description:ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

| PRJNA566427 | ENA

Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis

Project description:We applied ultra-low-input native ChIP-seq and profiled genome-wide H3K9me3 distribution in four germ cell types during spermatogenesis.

2020-07-17 | GSE137742 | GEO

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.

Project description:Whole-genome bisulfite sequencing (WGBS) is the current gold standard of methylome analysis. Post-bisulfite adaptor tagging (PBAT) is an increasingly popular WGBS protocol because of high sensitivity and low bias. PBAT originally relied on two rounds of random priming for adaptor-tagging of single-stranded DNA (ssDNA) to attain high efficiency but at a cost of library insert length. To overcome this limitation, we developed terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation as an alternative to random priming. In this method, TdT attaches adenylates to the 3'-end of input ssDNA, which are then utilized by RNA ligase as an efficient connector to the ssDNA adaptor. A protocol that uses TACS ligation instead of the second random priming step substantially increased the lengths of PBAT library fragments. Moreover, we devised a dual-library strategy that splits the input DNA to prepare two libraries with reciprocal adaptor polarity, combining them prior to sequencing. This strategy ensured an ideal base-color balance to eliminate the need for DNA spike-in for color compensation, further improving the throughput and quality of WGBS. Adopting the above strategies to the HiSeq X Ten and NovaSeq 6000 platforms, we established a cost-effective, high-quality WGBS, which should accelerate various methylome analyses.

| S-EPMC6736019 | biostudies-literature

Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

Project description:Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

| PRJNA566428 | ENA

Information recovery from low coverage whole-genome bisulfite sequencing.

Project description:The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ?30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future.

| S-EPMC4931220 | biostudies-literature

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.

Project description:DNA methylation plays a key role in epigenetic regulation of eukaryotic genomes. Hence the genome-wide distribution of 5-methylcytosine, or the methylome, has been attracting intense attention. In recent years, whole-genome bisulfite sequencing (WGBS) has enabled methylome analysis at single-base resolution. However, WGBS typically requires microgram quantities of DNA as well as global PCR amplification, thereby precluding its application to samples of limited amounts. This is presumably because bisulfite treatment of adaptor-tagged templates, which is inherent to current WGBS methods, leads to substantial DNA fragmentation. To circumvent the bisulfite-induced loss of intact sequencing templates, we conceived an alternative method termed Post-Bisulfite Adaptor Tagging (PBAT) wherein bisulfite treatment precedes adaptor tagging by two rounds of random primer extension. The PBAT method can generate a substantial number of unamplified reads from as little as subnanogram quantities of DNA. It requires only 100 ng of DNA for amplification-free WGBS of mammalian genomes. Thus, the PBAT method will enable various novel applications that would not otherwise be possible, thereby contributing to the rapidly growing field of epigenomics.

| S-EPMC3458524 | biostudies-literature

GENE-SWITCH Pig DNA methylation with Whole Genome bisulfite sequencing (WGBS)

Project description: Not available

| S-BSST612 | biostudies-other

GENE-SWITCH Chicken DNA methylation with Whole Genome bisulfite sequencing (WGBS)

Project description: Not available

| S-BSST618 | biostudies-other