characteristics.text: SAMN33699443
characteristics.characteristic: External Id
characteristics.text: National Coffee Research Center
characteristics.characteristic: INSDC center name
characteristics.text: 2023-03-30T00:50:31.520Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-03-31T12:19:44.433Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS17195708
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: PAIRED
characteristics.characteristic: Library_Layout
characteristics.text: PCR
characteristics.characteristic: Library_Selection
characteristics.text: METAGENOMIC
characteristics.characteristic: Library_Source
characteristics.text: MIGS/MIMS/MIMARKS.plant-associated
characteristics.characteristic: NCBI submission model
characteristics.text: MIMARKS.survey
characteristics.characteristic: NCBI submission model
characteristics.text: MIMARKS.survey.plant-associated.6.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS17195708
characteristics.characteristic: SRA accession
characteristics.text: 2021-12-14
characteristics.characteristic: collection_date
characteristics.text: Keywords: GSC:MIxS;MIMARKS:6.0
characteristics.characteristic: description
characteristics.text: Samples of coffee beans and mucilage were collected at the beginning (CD) and at the end of fermentation (CF) from each of the sampling units (farms), for gDNA extraction, was used a kit DNeasy Powerlyzer Powersoil (QIAGEN). DNA quantification was performed using a spectrophotometer NanoDrop™ 2000-Thermo Scientific™. For the deep sequencing of bacterial 16S rRNA genes, a fragment containing the V3 and V4 variable regions was amplified using the oligonucleotide primers 341F/805R. For fungal diversity, amplification of the ITS2 region was performed using the primers ITS3F/ITS4R. Sequencing was performed on the Illumina MiSeq platform, generating 300bp paired reads each. Sequence quality and classification analyses were performed using MOTHUR version 1.44 platform. Sequences for fungi and bacteria were taxonomically assigned according to the SILVA v138 database, using the VSEARCH method. The phylogenetic classification was performed using the Classifier tool from the RDP database.
characteristics.characteristic: design_description
characteristics.text: Coffee farm
characteristics.characteristic: env_broad_scale
characteristics.text: coffee mucilage liquid fraction
characteristics.characteristic: env_medium
characteristics.text: 16SFNACF12R1_1.fastq.gz
characteristics.characteristic: filename
characteristics.text: ITSFNACF12R2_2.fastq.gz
characteristics.characteristic: filename10
characteristics.text: ITSFNACF12R3_1.fastq.gz
characteristics.characteristic: filename11
characteristics.text: ITSFNACF12R3_2.fastq.gz
characteristics.characteristic: filename12
characteristics.text: 16SFNACF12R1_2.fastq.gz
characteristics.characteristic: filename2
characteristics.text: 16SFNACF12R2_1.fastq.gz
characteristics.characteristic: filename3
characteristics.text: 16SFNACF12R2_2.fastq.gz
characteristics.characteristic: filename4
characteristics.text: 16SFNACF12R3_1.fastq.gz
characteristics.characteristic: filename5
characteristics.text: 16SFNACF12R3_2.fastq.gz
characteristics.characteristic: filename6
characteristics.text: ITSFNACF12R1_1.fastq.gz
characteristics.characteristic: filename7
characteristics.text: ITSFNACF12R1_2.fastq.gz
characteristics.characteristic: filename8
characteristics.text: ITSFNACF12R2_1.fastq.gz
characteristics.characteristic: filename9
characteristics.text: fastq
characteristics.characteristic: filetype
characteristics.text: Colombia: Quindio
characteristics.characteristic: geo_loc_name
characteristics.text: Colombia
characteristics.characteristic: geo_loc_name_country
characteristics.text: Coffea arabica L.
characteristics.characteristic: host
characteristics.text: Illumina MiSeq
characteristics.characteristic: instrument_model
characteristics.text: 4.20472 N 75.79222 W
characteristics.characteristic: lat_lon
characteristics.text: METAGENOMIC
characteristics.characteristic: library_source
characteristics.text: AMPLICON
characteristics.characteristic: library_strategy
characteristics.text: food production metagenome
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1699855
characteristics.characteristic: organism
characteristics.text: ILLUMINA
characteristics.characteristic: platform
characteristics.text: MIMARKS Survey related sample from food production metagenome
characteristics.characteristic: title