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https://www.gene-switch.eu/

GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors.

Ensembl Rapid Release

Species
Accession
Assembly submitted by
Annotation Proteins Transcripts Softmasked genome Repeat library Other data View in browser
Gallus gallus (broiler - e107) GCA_016699485.1 Vertebrate Genomes Project GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsrapid.ensembl.org
Gallus gallus (jungle fowl - e102) GCA_000002315.5 Genome Reference Consortium GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsensembl.org
Gallus gallus (jungle fowl - e107) GCA_000002315.5 Genome Reference Consortium GTF, GFF3FASTAFASTAFASTARepeatmodelerFTP dumpsrapid.ensembl.org
Gallus gallus (layer - e107) GCA_016700215.2 Vertebrate Genomes Project GTF, GFF3FASTAFASTAFASTAFTP dumpsrapid.ensembl.org
Sus scrofa (bamei - e102) GCA_001700235.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
Sus scrofa (berkshire - e102) GCA_001700575.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
Sus scrofa (hampshire - e102) GCA_001700165.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
Sus scrofa (jinhua - e102) GCA_001700295.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
Sus scrofa (landrace - e102) GCA_001700215.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
Sus scrofa (largewhite - e102) GCA_001700135.1 Novogene GTF, GFF3FASTAFASTAFASTAFTP dumpsensembl.org
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Related Publications


Related Pipelines

Pipeline name
Assay type
Pipeline link
Pipeline documentation
Platform
TAGADA: Transcript And Gene Assembly, Deconvolution, Analysis RNA-seq https://github.com/FAANG/analysis-TAGADA#readme
Analysis of Chromosome Conformation Capture data (Hi-C) Hi-C https://github.com/FAANG/analysis-hic#readme
ATAC-seq peak-calling, QC and differential analysis pipeline ATAC-seq https://github.com/FAANG/analysis-atacseq#readme
GENE-SWitCH project Iso-Seq analysis pipeline Iso-seq https://github.com/FAANG/analysis-isoseq#readme
A small-RNA sequencing analysis pipeline smallRNA-seq https://github.com/FAANG/analysis-smrnaseq#readme
BayesRCO https://github.com/fmollandin/BayesRCO#readme
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Related Datasets

Study name
Species
Archive
Assay type
PRJEB41822 Sus scrofa ENA methylation profiling by high throughput sequencing
PRJEB41829 Gallus gallus ENA methylation profiling by high throughput sequencing
PRJEB41970 Sus scrofa ENA RNA-seq of total RNA
PRJEB42001 Sus scrofa ENA microRNA profiling by high throughput sequencing
PRJEB42025 Gallus gallus ENA RNA-seq of total RNA
PRJEB42041 Gallus gallus ENA microRNA profiling by high throughput sequencing
PRJEB42772 Sus scrofa ENA methylation profiling by high throughput sequencing
PRJEB42775 Gallus gallus ENA methylation profiling by high throughput sequencing
PRJEB44468 Sus scrofa ENA ATAC-seq
PRJEB44486 Sus scrofa ENA Hi-C
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Related Files

File name
Assay type
Experiment target
File size
Download
ERR10372888_1.fastq.gz 15.7GB
ERR10372888_2.fastq.gz 16.34GB
ERR10372889_1.fastq.gz 8.69GB
ERR10372889_2.fastq.gz 9.06GB
ERR12314066_1.fastq.gz RNA-seq of coding RNA histone_modification 1.19GB
ERR12314066_2.fastq.gz RNA-seq of coding RNA histone_modification 1.17GB
ERR12314067_1.fastq.gz RNA-seq of coding RNA histone_modification 821.73MB
ERR12314067_2.fastq.gz RNA-seq of coding RNA histone_modification 816.89MB
ERR12314068_1.fastq.gz RNA-seq of coding RNA input DNA 1018.08MB
ERR12314068_2.fastq.gz RNA-seq of coding RNA input DNA 993.25MB
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Related Organisms

BioSamples ID
Species
Sex
Breed
SAMEA10256251 TN60
SAMEA10256252 TN60
SAMEA10256253 TN60
SAMEA10256254 TN60
SAMEA10256255 TN60
SAMEA10256256 TN60
SAMEA10256257 TN60
SAMEA10256258 TN60
SAMEA10256259 TN60
SAMEA10256260 TN60
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Related Specimens

BioSamples ID
Material
Organism part/Cell type
Sex
Species
Breed
SAMEA10256411 specimen from organism liver Male Sus scrofa TN60
SAMEA10256412 specimen from organism liver Female Sus scrofa TN60
SAMEA10256413 specimen from organism liver Male Sus scrofa TN60
SAMEA10256414 specimen from organism liver Female Sus scrofa TN60
SAMEA10256415 specimen from organism liver Male Sus scrofa TN60
SAMEA10256416 specimen from organism liver Male Sus scrofa TN60
SAMEA10256417 specimen from organism liver Male Sus scrofa TN60
SAMEA10256418 specimen from organism liver Female Sus scrofa TN60
SAMEA10256419 specimen from organism liver Male Sus scrofa TN60
SAMEA10256420 specimen from organism liver Male Sus scrofa TN60
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Related Protocols

Protocol Name
University Name
Protocol Year
GENE SWitCH RRBS analysis WU 2021
GENE SWitCH WGBS analysis WU 2022
GENESWITCH WP2 isoseq gene annotation Roslin Institute (Edinburgh, UK) 2021
GENESWITCH WP2 isoseq gene annotation V2 Roslin Institute (Edinburgh, UK) 2022
srnaseq-processing INSERM-INRAE 2021
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