Description
This version 2 dataset contains 34 files in total with one (1) additional file, called "Culture-dependent Isolate table with taxonomic determination and sequence data.csv". The remaining files (33) are identical to version 1. The following is the information about the new file and its variables:
<b>Culture-dependent Isolate table with taxonomic determination and sequence data.csv</b>: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below:
IsolateNumber : unique number identify each isolate cultured
Time: season in which the sample was collected
Location: the specific name of the location
Habitat: type of habitat : either stream or peatland
State: state in the USA in which the specific location is located
Incubation_pH ID: pH of the medium during isolation of fungal cultures
Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity)
Sequence_quality: base call quality of the entire sequence used for blast analysis, if known
%_coverage: sequence coverage reported from GenBank
%_ID: sequence similarity reported from GenBank
Life_style : ecological life style if known
Phylum: phylogenetic phylum as indicated by Index Fungorum
Subphylum: phylogenetic subphylum as indicated by Index Fungorum
Class: phylogenetic class as indicated by Index Fungorum
Subclass: phylogenetic subclass as indicated by Index Fungorum
Order: phylogenetic order as indicated by Index Fungorum
Family: phylogenetic Family as indicated by Index Fungorum
ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5
Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software
Note: blank cells mean no data is available or unknown.
<b>Culture-dependent Isolate table with taxonomic determination and sequence data.csv</b>: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below:
IsolateNumber : unique number identify each isolate cultured
Time: season in which the sample was collected
Location: the specific name of the location
Habitat: type of habitat : either stream or peatland
State: state in the USA in which the specific location is located
Incubation_pH ID: pH of the medium during isolation of fungal cultures
Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity)
Sequence_quality: base call quality of the entire sequence used for blast analysis, if known
%_coverage: sequence coverage reported from GenBank
%_ID: sequence similarity reported from GenBank
Life_style : ecological life style if known
Phylum: phylogenetic phylum as indicated by Index Fungorum
Subphylum: phylogenetic subphylum as indicated by Index Fungorum
Class: phylogenetic class as indicated by Index Fungorum
Subclass: phylogenetic subclass as indicated by Index Fungorum
Order: phylogenetic order as indicated by Index Fungorum
Family: phylogenetic Family as indicated by Index Fungorum
ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5
Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software
Note: blank cells mean no data is available or unknown.
| Date made available | Nov 5 2020 |
|---|---|
| Publisher | University of Illinois Urbana-Champaign |
Keywords
- ITS1 forward reads
- Illumina
- bogs
- fens
- streams
- peatlands