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Protocols

SIGENAE specifications

Information


Unique identifier OMICS_32551
Name SIGENAE
Alternative name Système d'Information des GENomes des Animaux d'Elevage
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Registration required Yes
Maintained Yes

Additional information


http://www.sigenae.org/index.php?id=8

SIGENAE citations

 (37)
library_books

A microorganisms’ journey between plant generations

2018
Microbiome
PMCID: 5918900
PMID: 29695286
DOI: 10.1186/s40168-018-0459-7

[…] e sequence orientation using a homemade script. This stringent data trimming resulted in 9,592,312 reads. Trimmed sequences were then analyzed using the FROGS pipeline [] (bio-informatic workbench “X.SIGENAE” [http://www.sigenae.org/]). FROGS pre-process was performed with a custom protocol [] for archaea and fungi and with the FROGS standard protocol for bacteria reads. In this pre-process, bacte […]

library_books

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

2018
BMC Genomics
PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] ccession: E-MTAB-3522), and our brown trout and European whitefish assemblies to the corresponding species from the PhyloFish database [] (75,338 and 74,701 transcripts respectively; http://phylofish.sigenae.org/index.html). First, we assessed how well full-length transcripts were represented in our assemblies compared to the previous transcriptomes. Full-length transcript reconstruction in the pr […]

call_split

The development of contemporary European sea bass larvae (Dicentrarchus labrax) is not affected by projected ocean acidification scenarios

2017
PMCID: 5491573
PMID: 28751791
DOI: 10.1007/s00227-017-3178-x
call_split See protocol

[…] Heuer and Grosell ). The design of specific primers for each gene was performed using Primer3Plus software based on cDNA sequences available in public databases NCBI (https://www.ncbi.nlm.nih.gov) or SIGENAE (http://www.sigenae.org/) (Table ). The qPCR for each gene was performed using iQ™ SYBR® Green Supermix (Bio-Rad Laboratories, Hercule, USA) as previously described (Vanderplancke et al. ). Gl […]

call_split

Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray Finned Fish as the Outgroup

2017
Genome Biol Evol
PMCID: 5381532
PMID: 28082606
DOI: 10.1093/gbe/evw288
call_split See protocol

[…] hort length (<100 amino acids) were discarded.Next bowfin (Amia calva) data was added to data set I. The transcriptome data of the bowfin () was obtained from the PhyloFish database (http://phylofish.sigenae.org/). A Nucleotide BLAST search (r = 2, G = 2, E = 2, e-value cutoff of 1 × 10− 10) was performed with the bowfin contigs as the queries against the human (GRCh38) and zebrafish (Zv9) cDNA da […]

library_books

Sexually dimorphic gene expressions in eels: useful markers for early sex assessment in a conservation context

2016
Sci Rep
PMCID: 5034313
PMID: 27658729
DOI: 10.1038/srep34041

[…] Seven genes were selected based on a multi-tissue RNA-seq analysis originating from the PhyloFish project (http://phylofish.sigenae.org/index.html) that aimed at characterizing the transcriptome of 11 different tissues/organs in a wide variety of teleostean and holostean species, including Europen eel (NCBI BioProject PRJN […]

library_books

Comprehensive RNA Seq profiling to evaluate lactating sheep mammary gland transcriptome

2016
Sci Data
PMCID: 4932878
PMID: 27377755
DOI: 10.1038/sdata.2016.51

[…] on and differential expression analysis but also other publicly software combinations could be used for quantification and differential expression analysis: e.g. SigCufflinks (available at http://www.sigenae.org) or HTSeq for quantification, combined with edgeR or DESeq2 (ref. ) for the differential expression analyses. Based on power estimations () we recommend to use at least 5 replicates per co […]


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