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, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org |
Gallus gallus (jungle fowl - e102) | GCA_000002315.5 | Genome Reference Consortium | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | ensembl.org |
Gallus gallus (jungle fowl - e107) | GCA_000002315.5 | Genome Reference Consortium | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | rapid.ensembl.org |
Gallus gallus (layer - e107) | GCA_016700215.2 | Vertebrate Genomes Project | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | rapid.ensembl.org | |
Sus scrofa (bamei - e102) | GCA_001700235.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org | |
Sus scrofa (berkshire - e102) | GCA_001700575.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org | |
Sus scrofa (hampshire - e102) | GCA_001700165.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org | |
Sus scrofa (jinhua - e102) | GCA_001700295.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org | |
Sus scrofa (landrace - e102) | GCA_001700215.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org | |
Sus scrofa (largewhite - e102) | GCA_001700135.1 | Novogene | GTF, GFF3 | FASTA | FASTA | FASTA | FTP dumps | ensembl.org |
Pipeline name | Assay type | Pipeline link | Pipeline documentation | Platform |
---|---|---|---|---|
TAGADA: Transcript And Gene Assembly, Deconvolution, Analysis | RNA-seq | |||
Analysis of Chromosome Conformation Capture data (Hi-C) | Hi-C | |||
ATAC-seq peak-calling, QC and differential analysis pipeline | ATAC-seq | |||
GENE-SWitCH project Iso-Seq analysis pipeline | Iso-seq | |||
A small-RNA sequencing analysis pipeline | smallRNA-seq | |||
BayesRCO | ||||
Study name | Species | Archive | Assay type |
---|---|---|---|
Sus scrofa | ENA | methylation profiling by high throughput sequencing | |
Gallus gallus | ENA | methylation profiling by high throughput sequencing | |
Sus scrofa | ENA | RNA-seq of total RNA | |
Sus scrofa | ENA | microRNA profiling by high throughput sequencing | |
Gallus gallus | ENA | RNA-seq of total RNA | |
Gallus gallus | ENA | microRNA profiling by high throughput sequencing | |
Sus scrofa | ENA | methylation profiling by high throughput sequencing | |
Gallus gallus | ENA | methylation profiling by high throughput sequencing | |
Sus scrofa | ENA | ATAC-seq | |
Sus scrofa | ENA | Hi-C |
File name | Assay type | Experiment target | File size | Download |
---|---|---|---|---|
15.7GB | ||||
16.34GB | ||||
8.69GB | ||||
9.06GB | ||||
RNA-seq of coding RNA | histone_modification | 1.19GB | ||
RNA-seq of coding RNA | histone_modification | 1.17GB | ||
RNA-seq of coding RNA | histone_modification | 821.73MB | ||
RNA-seq of coding RNA | histone_modification | 816.89MB | ||
RNA-seq of coding RNA | input DNA | 1018.08MB | ||
RNA-seq of coding RNA | input DNA | 993.25MB |
BioSamples ID | Species | Sex | Breed |
---|---|---|---|
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 | |||
TN60 |
BioSamples ID | Material | Organism part/Cell type | Sex | Species | Breed |
---|---|---|---|---|---|
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Female | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Female | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Female | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 | |
specimen from organism | liver | Male | Sus scrofa | TN60 |
Protocol Name | University Name | Protocol Year |
---|---|---|
WU | 2021 | |
WU | 2022 | |
Roslin Institute (Edinburgh, UK) | 2021 | |
Roslin Institute (Edinburgh, UK) | 2022 | |
INSERM-INRAE | 2021 |