No. 0: Raw 16S rRNA fastq data files for Bocas hypoxia study

2020-06-14T19:53:27Z (GMT) by Jarrod Scott

This repository contains the RAW sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number PRJEB36632 (ERP119845).

Raw fastq data files are named using the root format RunQ_XYZ, where Q is the run number (1, or 2), X is the habitat type (Coral, Water, Sediment, Mat), YZ is the site (CC = Coral Cay; CR = Cayo Roldan), and in some cases a replicate number.

So...

Run01_CCR1_R2_001.fastq

...corresponds to the reverse reads (R2) of a Cayo Roldan (CR) coral sample (C), replicate #1, Run 1.

Raw fastq files are deposited here by Run.

We used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's protocol to extract community DNA from each sample.

Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome Resource at the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University).


We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA) and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 38 samples encompassing two sites and four habitat types

We generated sequence data for all 38 samples. In the first run (Run01), all samples were sequenced and, due to lower than average yield, several were re-sequenced (Run02).


This repo also contains the metadata files for submitting the trimmed data to the European Nucleotide Archive (ENA). Please do confuse this datasets with the dataset archived on the ENA (accession number PRJEB36632). In order to submit to the ENA, we had to first remove primers from the raw data and then upload the data along with these metadata files.


The first publication concerns the water samples only. If you are interested in those samples only they are also available in the WATER_ONLY.zip file.