Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted single-cell transcriptome readouts for high-throughput genetics and functional genomics

ABSTRACT: Targeted single-cell transcriptome readouts for high-throughput genetics and functional genomics

PROVIDER: PRJNA559094 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10885102_1.fastq.gz	Fastqsanger.gz
	SRR10885102_2.fastq.gz	Fastqsanger.gz
	SRR10885103_1.fastq.gz	Fastqsanger.gz
	SRR10885103_2.fastq.gz	Fastqsanger.gz
	SRR10885104_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 231

Similar Datasets

Targeted single-cell transcriptome readouts for high-throughput genetics and functional genomics

Project description:We show that targeted single-cell RNA-sequencing (TAP-seq) permits reliable mapping of cell (sub)types with as little as 100 reads per cell and reduces the sequencing costs for differential expression testing by a factor of 10-30, thereby enabling a cost-effective profiling of a large number of genotypes at the single cell level. We demonstrate the use of TAP-seq by generating comprehensive perturbation-based enhancer-target gene maps for 1.5% of the human genome.

2020-03-23 | GSE135497 | GEO

The EN-TEx Resource for Personal Functional Genomics

Project description:An overall goal of functional genomics has been to measure the impact of variants on molecular endophenotypes (e.g. gene expression levels or the degree of TF binding) and relate this to organismal traits and disease phenotypes. However, all the experiments to date have been described relative to a generic reference genome, significantly hobbling their interpretation. Here, we describe a strategy for finding significant relationships between disease variation and genomic annotation via personal functional genomics, by performing personal genome sequencing and paired functional genomics experiments, on the same individual.

2024-05-22 | PXD022787 | Pride

Functional genomics of SNRPA1/B2

Project description:Functional genomics of SNRPA1/B2

| PRJNA674889 | ENA

High-throughput functional comparison of promoter and enhancer activities

Project description:High-throughput functional comparison of promoter and enhancer activities

| PRJNA309883 | ENA

A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish.

Project description:The zebrafish is a popular model organism for studying development and disease, and genetically modified zebrafish provide an essential tool for functional genomic studies. Numerous publications have demonstrated the efficacy of gene targeting in zebrafish using CRISPR/Cas9, and they have included descriptions of a variety of tools and methods for guide RNA synthesis and mutant identification. However, most of the published techniques are not readily scalable to increase throughput. We recently described a CRISPR/Cas9-based high-throughput mutagenesis and phenotyping pipeline in zebrafish. Here, we present a complete workflow for this pipeline, including target selection; cloning-free single-guide RNA (sgRNA) synthesis; microinjection; validation of the target-specific activity of the sgRNAs; founder screening to identify germline-transmitting mutations by fluorescence PCR; determination of the exact lesion by Sanger or next-generation sequencing (including software for analysis); and genotyping in the F1 or subsequent generations. Using these methods, sgRNAs can be evaluated in 3 d, zebrafish germline-transmitting mutations can be identified within 3 months and stable lines can be established within 6 months. Realistically, two researchers can target tens to hundreds of genes per year using this protocol.

| S-EPMC5630457 | biostudies-literature

OA Functional Genomics

Project description:Functional genomics approaches to understand osteoarthritis

| EGAD00010001746 | EGA

High-throughput Discovery of Functional Protein Modifications by Hotspot Thermal Profiling

Project description:High-throughput Discovery of Functional Protein Modifications by Hotspot Thermal Profiling

2019-05-16 | MSV000083786 | MassIVE

Hip Osteoarthritis Functional Genomics

Project description:The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of hip osteoarthritis that culminates in the need for total joint replacement (TJR). This study is a feasibility pilot that integrates functional genomics data from diseased and non-diseased tissues of OA patients who have undergone TJR. For each tissue, we characterised epigenetic marks (methylation), gene transcription (RNASeq) and expression (quantitative proteomics). We also generated genotype data on the HumanCoreExome array for each individual. This data is part of a pre-publication release.

2018-05-14 | PXD006673 | Pride

Functional genomics of human colon organoids

Project description:Functional genomics of human colon organoids

| PRJNA589838 | ENA

A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1.

Project description:Substantial intrastrain variation at the nucleotide level complicates molecular and genetic studies in zebrafish, such as the use of CRISPRs or morpholinos to inactivate genes. In the absence of robust inbred zebrafish lines, we generated NHGRI-1, a healthy and fecund strain derived from founder parents we sequenced to a depth of ∼50×. Within this strain, we have identified the majority of the genome that matches the reference sequence and documented most of the variants. This strain has utility for many reasons, but in particular it will be useful for any researcher who needs to know the exact sequence (with all variants) of a particular genomic region or who wants to be able to robustly map sequences back to a genome with all possible variants defined.

| S-EPMC4174928 | biostudies-literature

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