Showing results for: [ Greenfield, Paul ]
18S rDNA, 16S rDNA, and diatom 18S v4 rDNA amplicons from sediment DNA collected from Vavouto Bay New Caledonia.
NiPERA - Metabarcoding reveals changes in benthic eukaryote and prokaryote community composition along a tropical sediment nickel gradient - Published 06 Jul 2020
The data describes the microbiome community of the coral Acropora mucricata following exposure to nickel and copper (separately) for 4 days under controlled laboratory conditions
NiPERA - The effect of dissolved copper and nickel on the adult coral Acropora muricata and its microbiome - Published 16 Apr 2019
Supporting 16S and ITS Illumina MiSeq data for the paper "Vineyard soil microbiome composition related to rotundone concentration in Australian cool climate ‘peppery’ Shiraz grapes" by Vadakattu et al... more.less
AWRI: Rotundone - - Published 26 Feb 2019
Raw RNA sequences from 27 individual greentail prawns (Metapenaeus bennettae) collected from St Vincent Gulf in South Australia in February 2016. Prawns were placed in tanks with either clean sediment... more or sediment spiked with 2 mg/kg of light-weight crude oil and exposed for 24 and 90 hrs before being transferred to clean sediment tanks for a further 90 hrs. Five prawns were removed from each tank at each of the different time periods. The aprrox. 10 mg of hepatopancreas was removed and place in RNAlater before freezing at -80. RNA libraries were prepared and sequenced by the Ramaciotti Centre (Sydeny, Australia), where libraries were prepared using 1 µg RNA from 27 individuals following Illumina protocols, and sequenced on two HiSeq2500 100bp single-end lanes in accordance with the manufacturer’s protocols. less
Chevron_GAB_Phase 2 - - Published 14 Dec 2018
RNA Seq reads (Illumina HiSeq 2500) from the liver and gill of spotted dragonet (Repomucenus calcaratus) exposed to either control conditions of 2 mg/kg unweathered crude oil. Fish tissues were colle... morected 24 and 90 hours into exposure as well as 20 and 90 hours into recovery.less
Chevron_GAB_Phase 2 - determining monitoring targets - Published 18 Jul 2018
This collection includes data to support the paper on the Kelpie software which reconstructs amplicons from metagenomes.
Specifically, the collection includes three zip files which includes pair-mer... moreged amplicon data for the 3 samples; the corresponding 16S-filtered WGS data and the original metagenomes.
The three formation water samples in the data labelled as:
W1, W2, W3 – and their respective basins/CSMB refs are in the Kelpie manuscript.less
Legacy data - Bacterial genomics - Published 26 Jun 2018
A data set of 16S rDNA reference sequences from coal seam environments.
Onshore Gas_General Prog Operations - - Published 23 Mar 2018
Whole genome sequencing was performed on Gamarada debralockiae gen. nov. sp. nov. Following sequence assemblies, contigs greater than 1,000 nucleotides were subjected to gene annotation and analysis. ... moreWe provide here the remaining contigs which were less than 1,000 nucleotides in length.less
Onshore Gas_General Prog Operations - - Published 30 Nov 2017
An in-house amplicon clustering and classification pipeline built around tools from USEARCH and RDP. It handles both 16S and 18S rDNA sequence data, and can be customised to use other reference sets a... morend marker genes.less
Onshore Gas_General Prog Operations - - Published 01 Nov 2017
Outdoor freshwater mesocosms spiked with varying concentrations of copper were sampled in order to profile microbial communities. Samples collected include water, sediment and cellulose baits. DNA was... more extracted from all sample types. In addition to this, RNA was extracted from sediment samples and reverse transcribed to get cDNA. The v4 region of the 16S ribosomal RNA gene was amplified using Earth Microbiome primers 515F and 806R.
The 16S rRNA gene amplicons were sequenced on the Illumina MiSeq platform with 250 base pair-end reads. Forward and reverse read alignments, quality filtering, chimera checking and OTU clustering were performed using USEARCH v9.
OTU sequences were submitted to GenBank, however, 130 were found to be too novel for submission and thus are made available here.less
Legacy data - Microbial community survey - Published 10 Oct 2017
Illumina Hi Seq reads from the hepatic transcriptome from individual immature male barramundi collected from Sandy Creek and Repulse Creeks
Estuarine Health Assessment - Investigations into fish health - Published 26 Apr 2017
Files associated with this project:
== MiSeq PE and Mitochrondrial reads ==
== HiSeq PE Data ==
= Mitochondrial genome =
... more- A_hancockii_mito_complete.fa (complete mitochrondrial genome)
= Nuclear genome =
- FRR3425_A_hancockii_noMITO_min_200.fasta (contigs > 200bp)
- FRR3425_A_hancockii_noMITO_belowCutoff_200.fasta (contigs < 200bp)
**Gene Calls (AUGUSTUS)**
- FRR3425.outfile (GFF)
- FRR3425.outfile.aa (Amino acid calls for genes)
- FRR3425.outfile.cdexons (Exons)
- FRR3425.outfile.codingseq (Coding seqs)
Legacy data - Fungal genomics - Published 07 Mar 2017
These files illumina sequencing reads representing the hepatic transcriptome of wild caught barramundi from Barratta Creek (353-360), N. Johnstone River (402-406) or the Wenlock Catchments (WC1-5; WC5... more5,56).less
Legacy data - Transcriptome characterization - Published 25 Nov 2016
Sphingobium yanoikuyae strain_B2_R1_001.fastq.gz
Sphingobium yanoikuyae strain_B2_R2_001.fastq.gz
*Velvet assembly as scaffolds or contigs*
*Annotation files - based on scaffolds*
Annotation Sphingobium yanoikuyae strain B2.faa
Annotation Sphingobium yanoikuyae strain B2.gff
*Putative cytochrome sequences*
*Putative plasmid sequence*
Sphingobium yanoikuyae strain B2 putative plasmid.zip - file contains the fasta, gene calls and BLAST matches for this contigless
Industrial Biotechnology - Stratetic Pro - Bacterial genomics - Published 19 Jul 2016
16S rRNA gene amplification and sequencing were performed to assess the effects of uranium on sediment microbial communities. A total of 12 treatments along a uranium concentration gradient of 0 - 4,0... more00 mg/kg were interrogated, with four replicates per treatment. Data here include: raw MiSeq sequences (paired-end 250 base reads) as well as a mapping file for demultiplexing and a fasta file containing sequences of OTUs not deposited at DDBJ/ENA/GenBank (due to poor sequence similarity with existing entries). less
Estuarine Health Assessment - Next generation sequencing - Published 13 May 2016
These files illumina sequencing reads representing the hepatic transcriptome of wild caught barramundi from the Daintree River (fish numbers 2-7) or the Tully River (fish numbers 97-104).
Estuarine Health Assessment - Next generation sequencing - Published 03 Sep 2015