Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

ABSTRACT: Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

PROVIDER: PRJNA316188 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3289640.fastq.gz	Fastqsanger.gz
	SRR3289650.fastq.gz	Fastqsanger.gz
	SRR3289641.fastq.gz	Fastqsanger.gz
	SRR3289642.fastq.gz	Fastqsanger.gz
	SRR3289652.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Input Strategy for Improving Analysis of ChIP-exo Data and Beyond [RNA-Seq]

Project description:Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data.

2016-08-24 | GSE79564 | GEO

PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

Project description:Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.

2016-08-24 | GSE79563 | GEO

Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-08-24 | GSE79565 | GEO

PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond.

| S-EPMC5137431 | biostudies-literature

Homo sapiens

Project description:Input Strategy for Improving Analysis of ChIP-exo Data and Beyond [RNA-Seq]

| PRJNA316189 | ENA

Homo sapiens

Project description:PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

| PRJNA316190 | ENA

miRNAs in adipose tissue derived exosomes (Exo-AT) and adipose stem cells derived exosomes (Exo-ADSCs)

Project description:The emerging evidences support that exosome cargo miRNAs function as important regulators in cell differentiation. Therefore, in order to figure out the mechanism that Exo-AT mediated adipogenesis, we profiled miRNAs in Exo-AT using high-throughput sequencing (miRNA-seq). After trimming low-quality reads, contaminants, adaptors, and reads smaller than 15 nt, the remaining reads were mapped to merged pre-miRNA data bases. To identify the conserved miRNAs in Exo exosomes, miRNAs were aligned to miRBase v21. 148 and 154 types of known miRNAs in Exo-ADSCs and Exo-AT, respectively, were identified in the two replicates. Among these miRNAs, 103 miRNAs were simultaneously detected in both Exo-ADSCs and Exo-AT. Compared to Exo-ADSCs, 45 conserved miRNAs were enriched (expressed ≥ 2 folds, FDR<0.05) in Exo-AT. KEGG Pathway analysis was performed for the targets of the most 20 enriched miRNAs in Exo-AT (compared with Exo-ADSCs) to determine their potential function. Data showed that pathways that regulate adipogenesis such as Wnt signaling pathway, Insulin signaling pathway, MAPK signaling pathway, TGF-ß signaling pathway were enriched significantly for targets of Exo-AT miRNAs. Furthermore, 14 of 45 enriched miRNAs in Exo-AT (31.11%, such as miR-30a-5p, miR-148a-3p) were reported to participate in regulation of adipogenesis while 8 miRNAs (17.78%, such as miR-93-5p, miR-150-3p) that negatively control osteoblastic differentiation of MSC have been described.

2018-12-01 | GSE92313 | GEO

miRNA array experiment of NC-Exo and GATA4-Exo

Project description:miRNA array experiment of NC-Exo and GATA4-Exo

| PRJNA592052 | ENA

The expression level of miRNAs in Control-EXO and RIPC-EXO

Project description:To explore the possibility of miRNA(s) contributing to the cardioprotection induced by plasma exosomes at the late phase of RIPC, we performed a miRNA profiling assay (763 rat miRNAs) comparing the differences between RIPC-exo and Control-exo using Illumina HiSeq 2500 high-throughput sequencing.

2021-12-23 | GSE182675 | GEO

Simplified ChIP-exo assays

Project description:Simplified ChIP-exo assays

| PRJNA434276 | ENA