SAB_isolates_assembly_annotation

Four organisms were isolated from shelf waters of the South Atlantic Bight; a diatom and coccolithophore from the inner shelf (C. closterium UGA8 and G. oceanica) and the outer shelf (C. closterium UGA4 and G. huxleyi, formerly E. huxleyi). Isolates were grown in steady state high and low iron treatments, with an additional 24hr iron amendment treatment. A hybrid De Novo transcriptome was created with rnaSPAdes for each isolate using Illumina NextSeq and PacBio IsoSeq sequencing. Notebooks associated with this data are on GitHub. Organism codes: 08 : Inner shelf C. closterium UGA8 06: Inner shelf G. oceanica 04: Outer shelf C. closterium UGA4 13: Outher shelf G. huxleyi Treatment codes: pFe19: High Iron pFe21_9: Low Iron add_back: Iron amendment File descriptions: transcriptome_assemblies : zip folder of hybrid assemblies for each isolate using rnaSPAdes assembly04.fasta - C. closterium UGA4 assembly06.fasta - G. oceanica assembly08.fasta - C. closterium UGA8 assembly13.fasta - G. huxleyi predictORFs : zip folder of predicted open reading frames from each assembly using TransDecoder. .pep files are amino acids and .fasta are nucleotide sequences for each predicted ORF predict_orfs_04.pep, predict_orfs_04.fasta - C. closterium UGA4 predict_orfs_06.pep, predict_orfs_06.fasta - G. oceanica predict_orfs_08.pep, predict_orfs_08.fasta - C. closterium UGA8 predict_orfs_13.pep, predict_orfs_13.fasta - G. huxleyi orf_count : zip folder of salmon quantified predicted open reading frames named by isolate code, treatment, replicate. C. closterium UGA4: 04add_backA_quant.sf, 04add_backB_quant.sf 04pFe21_9A_quant.sf, 04pFe21_9B_quant.sf, 04pFe21_9C_quant.sf G. oceanica: 06add_backA_quant.sf, 06add_backB_quant.sf, 06add_backC_quant.sf 06pFe19A_quant.sf, 06pFe19B_quant.sf, 06pFe19C_quant.sf 06pFe21_9A_quant.sf, 06pFe21_9B_quant.sf, 06pFe21_9C_quant.sf C. closterium UGA8: 08add_backB_quant.sf, 08add_backC_quant.sf 08pFe19A_quant.sf, 08pFe19B_quant.sf, 08pFe19C_quant.sf 08pFe21_9A_quant.sf, 08pFe21_9B_quant.sf, 08pFe21_9C_quant.sf G. huxleyi: 13add_backA_quant.sf, 13add_backB_quant.sf, 13add_backC_quant.sf 13pFe19A_quant.sf, 13pFe19B_quant.sf, 13pFe19C_quant.sf 13pFe21_9A_quant.sf, 13pFe21_9B_quant.sf, 13pFe21_9C_quant.sf annootations : zip folder of eggNOG-mapper functional annotations for each transcriptome eggnog_anno_04 - C. closterium UGA4 eggnog_anno_06 - G. oceanica eggnog_anno_08 - C. closterium UGA8 eggnog_anno_13 - G. huxleyi