Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: A novel Nested Amplicon Sequencing approach targetting multiple loci from pinned specimens

PROVIDER: PRJNA478798 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7465240_1.fastq.gz	Fastqsanger.gz
	SRR7465240_2.fastq.gz	Fastqsanger.gz
	SRR7465250_1.fastq.gz	Fastqsanger.gz
	SRR7465250_2.fastq.gz	Fastqsanger.gz
	SRR7465260_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 282

Similar Datasets

Amplicon sequencing of a K562 cell line model with a patient-based t(3;8) translocation following CRISPR treatment

Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).

2021-07-26 | E-MTAB-9937 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run6)

Project description:Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish. Each loci has a control, where no Cas9/sgRNA were injected. This is amplicon sequencing with Illumina, after PCR amplification. Data was processed with ampliCan R package version 1.1.1.

2017-12-25 | E-MTAB-6310 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 7)

2017-12-15 | E-MTAB-6355 | biostudies-arrayexpress

Capturing pairwise and multi-way chromosomal conformations using C-walks

Project description:Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs), are highly conserved between cell types and species. Whether pairwise loops synergize to form higher order structures is still unclear. Here we develop a conformation capture approach to study higher order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains. The data captured a hierarchical chromosomal structure at varying scales. Inter-chromosomal contacts constitute only 7-10% of the pairs and are restricted by the TAD structure of the interfacing chromosomes. About half of the C-walks stay within one chromosome, and almost half of these are restricted to intra-TAD spaces. Analysis of nested topological motifs suggests hierarchical chromosomal structure is present also within TADs. Targeted analysis of thousands of 3-walks anchored at strongly expressed genes support nested, rather than hub-like, chromosomal topology at active loci. Polycomb-repressed HOX domains are shown by the same approach to form synergistic hubs. Together, the data suggest that chromosomal territories, TADs, and intra-TAD loops are primarily driven by nested, possibly dynamic, pairwise contacts.

2016-02-04 | GSE77553 | GEO

Project description:A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)

| PRJNA616106 | ENA

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 9)

2017-12-15 | E-MTAB-6357 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 10)

2017-12-15 | E-MTAB-6358 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 8)

2017-12-15 | E-MTAB-6356 | biostudies-arrayexpress

DNA hypomethylation restrains early antitumor immunity in prostate cancer [ChIP-seq and CUT&RUN]

Project description:Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution single cell DNA methylation sequencing in prostate cancer, we identify 40 core hypomethylation domains, consistently hypomethylated across tumor cells and arising at early stages of malignancy. Transcriptionally silenced genes within these domains are enriched for immune-related genes; nested among repressive domains are small loci with preserved methylation, encoding cell proliferation genes that escape silencing. Prominent among hypomethylation-silenced genes is a gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells, and four IFI16-related interferon-inducible genes implicated in innate immunity. Re-expression of CD1 or IFI16 murine orthologs in immunocompetent mice abrogates prostate tumorigenesis, accompanied by activation of anti-tumor immunity. Thus, early epigenetic changes in cancer may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for circulating tumor cells.

2023-06-14 | GSE209967 | GEO

Massively parallel quantification of the regulatory effects of non-coding genetic variation [STARR-seq]

Project description:We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter-gene expression assay. As demonstration, we have measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. We found that, in agreement with previous reports, most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify likely causal regulatory haplotypes that contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses. 104 candidate regulatory elements from 95 individuals were resequenced using Illumina custom amplicon sequencing. We then cloned the resulting DNA fragments into a massively parallel reporter assay to quantify allele-specific regulatory activity from that population. SNP-fdr.txt contains output of significance evaluation haplotype.fasta.gz contains the reference used to generate alignment files

2015-06-15 | E-GEOD-68331 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data