EpiDB is a platform for sharing processed NGS data useful as reference
information and data reuse to link genotype to phenotype in domestic
food animal species.
Created in 2014, EpiDB is a smart, interactive repository and platform for searching and analyzing domestic food animal epigenetic and gene expression data. The main idea of this web-based resource was to make functional next-generation sequencing (NGS) data for chicken, cattle, pig, horse, and sheep available as pre-processed and summarized genomic information to the scientific community, as well as to promote the re-use of existing data.
Functions already available are (legacy data):
- Querying the meta data database to facilitate data re-use;
- Downloads available for tissue specific, whole transcriptome expression baseline levels;
- Access to a dynamic gene expression atlas;
- Datasets for cattle, pig, chicken, sheep, and horse.
Future:
- Add new data from cattle FAANG project;
- Provide tissue-specific allele specific expression;
- Provide full epigenetic expression levels, as miRNA and methylation;
- Facilitate all livestock species;
- Incorporate ChIPseq and regulation information;
- Expand to additional species and data types.
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Data counts in current EpiDB version
Species | Tissues | Genes | Data set | Expression counts |
Cattle | 69 | 45,060 | 4 | 101,898,860 |
Chicken | 0 | 0 | 0 | 0 |
Horse | 0 | 0 | 0 | 0 |
Pig | 0 | 0 | 0 | 0 |
Sheep | 0 | 0 | 0 | 0 |
Most recent data updates
Data realm | Last updates |
count types | 2023-06-27 15:44:22 |
data src | 2023-11-30 09:41:52 |
exp types | 2023-06-27 15:35:02 |
expr counts | 2023-11-30 09:41:52 |
gene info | 2023-07-21 02:57:48 |
miRBase | 2023-11-10 21:08:12 |
sample conditions | 2023-09-06 11:17:30 |
species info | 2022-12-18 18:18:18 |
tissue link | 2023-09-06 16:42:20 |
tissue linksrc | 2023-07-18 22:40:59 |
users | 2023-04-06 21:43:50 |
Recent web tools developments
- EpiDB.animalgenome.org/data (Nov 30, 2023)
- EpiDB.animalgenome.org/tools (Nov 30, 2023)
- EpiDB.animalgenome.org/freqct (Nov 29, 2023)
- EpiDB.animalgenome.org/dev/login (Nov 02, 2023)
- EpiDB.animalgenome.org/dev/userset (Nov 01, 2023)
- EpiDB.animalgenome.org/dev/maptrait (Nov 01, 2023)
- EpiDB.animalgenome.org/dev/entry (Oct 31, 2023)
- EpiDB.animalgenome.org/resource (Sep 26, 2023)
- EpiDB.animalgenome.org/atlas (Sep 26, 2023)
- EpiDB.animalgenome.org/exprcounts (Sep 26, 2023)
- EpiDB.animalgenome.org/index (Sep 26, 2023)
- EpiDB.animalgenome.org/dev/index (May 19, 2023)
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