Showing results for: [ Midgley, David ]
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
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
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
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