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Author: asaravia-butler

GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv

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+name,species,strain,ensemblVersion,ref_source,fasta,gtf,taxon,annotations,genelab_annots_link,genelab_annots_info_link
+ARABIDOPSIS,Arabidopsis thaliana,,58,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-58/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-58/gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.58.gtf.gz,3702,org.At.tair.db,,
+BACSU,Bacillus subtilis,subsp. subtilis 168,58,ensembl_bacteria,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-58/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/dna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-58/gtf/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.58.gtf.gz,224308,org.MeSH.Bsu.168.db,,
+BRARP,Brassica rapa,,58,ensembl_plants,,,,,,
+WORM,Caenorhabditis elegans,,111,ensembl,https://ftp.ensembl.org/pub/release-111/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz,https://ftp.ensembl.org/pub/release-111/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.111.gtf.gz,6239,org.Ce.eg.db,,
+ZEBRAFISH,Danio rerio,,111,ensembl,,,7955,org.Dr.eg.db,,
+FLY,Drosophila melanogaster,,111,ensembl,,,7227,org.Dm.eg.db,,
+ERCC,,,,ThermoFisher,,,,,,
+ECOLI,Escherichia coli,str. K-12 substr. MG1655,58,ensembl_bacteria,,,83333,org.EcK12.eg.db,,
+HUMAN,Homo sapiens,,111,ensembl,https://ftp.ensembl.org/pub/release-111/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz,9606,org.Hs.eg.db,,
+MOUSE,Mus musculus,,111,ensembl,https://ftp.ensembl.org/pub/release-111/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-111/gtf/mus_musculus/Mus_musculus.GRCm39.111.gtf.gz,10090,org.Mm.eg.db,,
+,Mycobacterium marinum,LHM4,58,ensembl_bacteria,,,,,,
+ORYLA,Oryzias latipes,,111,ensembl,,,,,,
+RAT,Rattus norvegicus,,111,ensembl,,,10116,org.Rn.eg.db,,
+YEAST,Saccharomyces cerevisiae,S288C,111,ensembl,,,559292,org.Sc.sgd.db,,
+STAA8,Staphylococcus aureus,UAMS-1,58,ensembl_bacteria,,,,,,
+,Streptococcus mutans,UA159,58,ensembl_bacteria,,,,,,
+BRADI,Brachypodium distachyon,,58,ensembl_plants,,,15368,,,
+ORYSJ,Oryza sativa,Japonica,58,ensembl_plants,,,4530,BSgenome.Osativa.MSU.MSU7,,