Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq dynamic transcriptomic pipeline

ABSTRACT: Purpose: Develop an analytical pipeline for dynamic RNA-seq experiments and highlight the importance of considering surgery effect in MI-induced models Methods: Mice have undergone surgery, hearts were harvested and RNA was extracted, sequenced and analyzed by DESeq2 R package. Differentially expressed transcripts were clustered by WGCNA and then analyzed to identify enriched biological processes and transcription factors. Results: Our pipeline enabled the detection of 1027 DETs. Enriched biological processes were mainly cell signilisation and inflammatory related. IL-6 was found as a key controller of the identified TFs and DETs. Immune cells were recruited to the myocardium later post surgery and some possessed phenotypic changes.

ORGANISM(S): Mus musculus

PROVIDER: GSE127244 | GEO | 2019/04/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Castanet pipeline validation study

Project description:Castanet pipeline validation study

| PRJEB77004 | ENA

iMir: An integrated pipeline for high-throughput miRNA-Seq data analysis

Project description:We report a novel modular pipeline (iMir) for comprehensive analysis of miRNA-Seq data, from linker removal and sequence quality check to differential expression and biological target prediction, integrating multiple open source modules and resources linker together in an automated flow.

2013-12-11 | GSE40617 | GEO

iMir: An integrated pipeline for high-throughput miRNA-Seq data analysis

2013-12-11 | E-GEOD-40617 | biostudies-arrayexpress

RNA-seq dynamic transcriptomic pipeline

Project description:RNA-seq dynamic transcriptomic pipeline

| PRJNA524471 | ENA

SPOROS: A pipeline to analyze DISE/6mer Seed Toxicity

Project description:The SPOROS pipeline is a read-based sequence analysis pipeline for studying 6mer Seed Toxicity in mouse and human RNA-seq data.

2021-08-22 | GSE182222 | GEO

IS-Seq: a novel bioinformatics pipeline for integration sites analysis

Project description:IS-Seq pipeline is developed,and 4 data sets are used to compare different abundance estimation methods of this pipeline

2023-08-08 | GSE203211 | GEO

Zonkey pipeline

Project description:Zonkey: A fast, simple, accurate and sensitive pipeline to genetically identify equid F1-hybrids in archaeological assemblages

| PRJEB15037 | ENA

Comprehensive profiling of extracellular RNA in HPV-induced cancers using an improved pipeline for small RNA-seq analysis

Project description:Extracellular RNAs (exRNAs) have attracted great attention due to their essential role in cell-to-cell communication as well as their potential as non-invasive disease biomarkers. Recent studies have shown that exRNAs are associated with a variety of biological processes. Thus, the study of deregulated exRNAs would provide insight into disease progression. At present, there is no consensus on the best method to profile exRNA expression, which leads to significant variability across studies. To address this issue, we established a robust pipeline for comprehensive profiling of small exRNAs isolated from cell culture. With this method, we performed small RNA sequencing of exosomes (EXOs), microvesicles (MVs) and source cells from 14 cancer cell lines.

2020-09-29 | GSE158659 | GEO

Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

Project description:Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe customized six-frame translation database and for the first time applied this pipeline to large-scale identification of NCPs in both monocot and dicot plants. Altogether, 1,993 and 1,860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. The NCPs showed distinct characteristics compared to canonical peptides and can be derived from introns, 3’UTRs, 5’UTRs, junctions and intergenic regions. These results revealed that non-canonical translation or cryptic translation events occur more universally than previously thought. In addition, maize NCPs were found enriched within the regions associated with phenotypic variation or regions under domestication selection, indicating their potential function in plant genetic regulations of complex traits and evolution. Summarily, this study provides the first unbiased and global view of plant NCPs. The identification of large-scale NCPs in both monocot and dicot plants reveals that a much larger portion of the plant genome can be translated biologically functional molecules, which has important implications in functional genomic studies. The present study also provides a useful resource for the characterization of more hidden NCPs in other plants.

2020-08-11 | PXD017080 | Pride

Optimized RiboMethSeq pipeline

Project description:Holistic optimization of bioinformatic analysis pipeline for detection and quantification of 2’-O-methylations in RNA by RiboMethSeq

| PRJEB35565 | ENA

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