Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formica exsecta

ABSTRACT: Formica exsecta Transcriptome or Gene expression

PROVIDER: PRJNA213662 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2080395_1.fastq.gz	Fastqsanger.gz
	SRR2080395_2.fastq.gz	Fastqsanger.gz
	SRR2080396_1.fastq.gz	Fastqsanger.gz
	SRR2080396_2.fastq.gz	Fastqsanger.gz
	SRR2080487_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Formica exsecta

Project description:Formica exsecta Transcriptome or Gene expression

| PRJNA198828 | ENA

Formica exsecta

Project description:Formica exsecta overview

| PRJNA202941 | ENA

Formica exsecta isolate:Colony F162

Project description:Formica exsecta isolate:Colony F162 Genome sequencing and assembly

| PRJNA393850 | ENA

Wolbachia endosymbiont of Formica exsecta

Project description:Wolbachia endosymbiont of Formica exsecta Genome sequencing and assembly

| PRJNA436771 | ENA

Formica exsecta

Project description:Exogenous material associated with F. exsecta

| PRJNA412141 | ENA

Formica exsecta

Project description:Changes in gene methylation and expression accompany caste specialization and ageing in a social insect

| PRJDB6378 | ENA

Formica exsecta

Project description:Ant and nest microbiome

| PRJNA691440 | ENA

Formica podzolica

Project description:Formica podzolica (Formica podzolica), iyForPodz1

| PRJNA1105408 | ENA

Formica podzolica

Project description:Formica podzolica (Formica podzolica) genomic and transcriptomic data

| PRJNA1105409 | ENA

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta.

Project description:Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.

| S-EPMC5701548 | 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