Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq

ABSTRACT: A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq

PROVIDER: PRJNA574622 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10195100.fastq.gz	Fastqsanger.gz
	SRR10195101.fastq.gz	Fastqsanger.gz
	SRR10195102.fastq.gz	Fastqsanger.gz
	SRR10195103.fastq.gz	Fastqsanger.gz
	SRR10195104.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq

Project description:The immune system operates at the scale of the whole organism in mammals. We currently lack experimental approaches to systematically track and study organism-wide molecular processes in mice. Here we describe an integrated toolkit for measuring gene expression in whole tissues, 3-prime mRNA extension sequencing, that is applicable to most mouse organs and any mouse model of interest. Further, the methods of RNA-seq described in this protocol are broadly applicable to other sample types beyond whole organs, such as tissue samples or isolated cell populations. We report procedures to collect, store and lyse a dozen organ types using conditions compatible with the extraction of high-quality RNA. In addition, we detail protocols to perform high-throughput and low-cost RNA extraction and sequencing, as well as downstream data analysis. The protocol takes 5 d to process 384 mouse organs from collecting tissues to obtaining raw sequencing data, with additional time required for data analysis and mining. The protocol is accessible to individuals with basic skills in (i) mouse perfusion and dissection for sample collection and (ii) computation using Unix and R for data analysis. Overall, the methods presented here fill a gap in our toolbox for studying organism-wide processes in immunology and physiology.

2019-10-01 | GSE138103 | GEO

A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq.

| S-EPMC7872736 | biostudies-literature

Whole-organism C. elegans L2 GRH-1 ChIP-seq

Project description:Whole-organism C. elegans L2 GRH-1 ChIP-seq

| PRJNA881263 | ENA

RNA-seq studies

Project description:RNA-seq studies

| PRJNA704569 | ENA

scRNA-seq studies

Project description:scRNA-seq studies

| PRJNA648132 | ENA

Calcium Toolkit genes expression in the zebrafish brain

Project description:Zebrafish are well suited for in vivo calcium imaging because the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling.

2019-03-05 | GSE127335 | GEO

FindingNemo Toolkit

Project description:A toolkit for ultra-long sequencing on ONT platforms

| PRJEB76809 | ENA

Australia dry land whole organism

Project description:Australia dry substrate whole organism Raw sequence reads

| PRJNA448205 | ENA

KAS-Analyzer: an integrated toolkit for exploring KAS-seq data

Project description:KAS-Analyzer: an integrated toolkit for exploring KAS-seq data

| PRJNA834084 | ENA

Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]

Project description:Whole-organism C. elegans L2/L3 NHR-23 ChIP-seq [NHR23_ChIPseq]