An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA539985 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, the current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type specific gene regulatory programs in complex tissues, by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain. *** Processed files of brain cells can be downloaded from: https://github.com/cxzhu/Paired-seq/tree/master/matrices/ - Compressed files for cell-gene/bin-counts matrices of Adult Cerebral Cortex cells only. - Compressed files for cell-gene/bin-counts matrices of merged Fetal and Adult brain cells. - Metadata files of sequenced cells are inside the compressed files. - Cluster/Ident to Annotation information available from the GitHub page.
2019-11-01 | GSE130399 | GEO
Project description:Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells. We demonstrate the utility of Paired-seq for analyzing the dynamic and cell-type-specific gene regulatory programs in complex tissues by applying it to mouse adult cerebral cortex and fetal forebrain. The joint profiles of a large number of single cells allowed us to deconvolute the transcriptome and open chromatin landscapes in the major cell types within these brain tissues, infer putative target genes of candidate enhancers, and reconstruct the trajectory of cellular lineages within the developing forebrain.
| S-EPMC7231560 | biostudies-literature
Project description:We report a method enabling simultaneous, ultra-high throughput single-cell-barcoding, of millions of cells for targeted single cell analysis of proteins and RNAs. This method termed Quantum Barcoding (QBC) circumvents the need to isolate single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette) cell-specific codes are added to each tagged molecule within cells. This is accomplished through sequential rounds of the well-established process of classic “split-pool synthesis”. We demonstrate the utility of this currently research use only technology in multiple model systems.
2019-05-07 | GSE130784 | GEO
Project description:To investigate differentially expressed lncRNAs,circRNAs,miRNAs and mRNAs in synovium of human temporomandibular joint osteoarthritis (TMJOA), we performed RNA high-throughput sequencing in synovium of human TMJOA. We then performed gene expression profiling analysis using data obtained from RNA-seq .
2022-06-07 | GSE205389 | GEO
Project description:We have developed an ultra effective method of generating extra multipotent (xpotent) cells which have differentiation potential more than limited cell types, by the mechanism of ultrasound-directed permeation of environmental transition-guided cellular reprogramming (Entr).
2019-09-09 | GSE86646 | GEO
Project description:Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissue lack resolution due to the cellular heterogeneity. Here, we describe an ultra-high throughput method for single-cell joint profiling of histone modifications and transcriptome that could produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our results demonstrate a general approach for comprehensive analysis of chromatin state and gene regulation in complex tissues and provide insights into the gene regulatory processes in major neuron cell types in the mouse.
2020-12-15 | GSE152020 | GEO
Project description:We have developed an ultra effective method of generating extra multipotent (xpotent) cells which have differentiation potential more than limited cell types, by the mechanism of ultrasound-directed permeation of environmental transition-guided cellular reprogramming (Entr).
2019-09-09 | GSE86647 | GEO
Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples. Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources. Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.
2018-03-06 | GSE111000 | GEO
Project description:Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing
| PRJNA713314 | ENA
Project description:Single-base resolution DNA methylomes have been accomplished for both Arabidopsis and human cells which have high genome methylation levels by Illumina ultra-high-throughput bisulfite sequencing technology (MethylC-Seq). Here by combining MethylC-Seq and biological replicate strategies we generated single-base resolution methylome for the silkworm which has low genome methylation levels like other insects. Our conservative estimation showed that methylcytosines (mCs) accout for about 0.11% of genomic cytosines, exclusively in CG context. The CG methylation is significantly enriched in gene bodies and positively correlated with gene expression levels, suggesting its positive role in gene transcription in silkworms. However, the well-documented functions of methylation on promoters and rDNAs in plants and mammals do not seem to have effects in insects. Methylated genes are enriched in functions involved in cellular metabolism and biosynthesis. Small RNA (smRNA) loci are also significantly enriched in gene bodies, and moreover, the smRNA loci and the predicted target sites of microRNA have high level of CG methylation, indicating functional involvement of smRNAs in the genic methylation This first methylome for silkworms provides a foundation for further studies on the epigenetic gene regulation of silkworms’ or even insects’ gene methylation. Each silk gland of 5th instar larvae of two individuals (called Biological Replicate 1 and 2, respectively) of the silkworm (Bombyx mori) strain Dazao was ground into powder in liquid nitrogen. Half of the powder from each silk gland was used to extract total DNAs using DNeasy Blood & Tissue Kit (Qiagen) and another half was used to extract total RNAs using RNeasy Mini Kit (Qiagen). We sequenced bisulfite-treated total DNA extracted from the silk glands of the two individuals, using Illumina Ultra-High-Throughput Sequencing, generating the Single-Base Resolution Methylomes. To reveal functional consequences of gene body methylation, we generated expression profiles for the two individuals’ silk glands using Digital Gene Expression tag profiling (DGE) technology, which combines classic SAGE (Serial Analysis of Gene Expression) and Illumina ultra-high-throughput sequencing technology.
2010-04-09 | E-GEOD-18315 | biostudies-arrayexpress