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