WGS of Environmental DNA from paper mill waste: Primary_wastewater_sl... - SRA

SRX3580062: WGS of Environmental DNA from paper mill waste: Primary_wastewater_sludge (paired-end_reads and assmebly)
1 ILLUMINA (Illumina HiSeq 4000) run: 75.5M spots, 22.8G bases, 9.6Gb downloads

Design: DNA library preparations and sequencing reactions were conducted at GENEWIZ, Inc.(NEB NextUltra DNA Library Preparation kit was used following the manufacturer s recommendations; the genomic DNA was fragmented by acoustic shearing with a Covaris S220 instrument. The DNA was end repaired and adenylated. Adapters were ligated after adenylation of the 3 ends. Adapter-ligated DNA was indexed and enriched by limited cycle PCR. The DNA library was validated using TapeStation and was quantified using Qubit 2.0 Fluorometer. The sequencing libraries will be multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell will be loaded on the Illumina HiSeq instrument according to manufacturer s instructions. The samples will be sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bsl2fastq v. 2.17 program. One mis-match was allowed for index sequence identification.

Submitted by: Anupama Sharan's shared submissions (anupama1235's shared submissions)

Study: paper pulp sludge enviromental metagenome

PRJNA416145 • SRP130818 • All experiments • All runs

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This Bioproject describes sampling and consequent metagenomic analysis of the microbial community inhabiting primary wastewater sludge of a coastal BC paper mill. The metagenomic DNA was used for creating a fosmid library that was mined for carbohydrate active enzymes (cAZymes) using a high throughput functional screen and selected clones applied for consolidated bioprocess development. In-silico analysis of the metagenomic data using several bioinformatics pipelines, most importantly Metapathways, was also conducted to complement experimental findings. The metagenome was taxonomically binned and functionally compared to data from other biomass waste environments. This project establishes proof of concept of application of metagenomics to circular bioeconomy development.

Sample: Pulp and paper sludge metagenome sample from coastal BC mill

SAMN07843559 • SRS2849407 • All experiments • All runs

Organism: paper pulp metagenome

Library:

Name: PPS_raw_reads

Instrument: Illumina HiSeq 4000

Strategy: WGS

Source: METAGENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 75.5M spots, 22.8G bases, 9.6Gb

Run	# of Spots	# of Bases	Size	Published
SRR6490213	75,488,683	22.8G	9.6Gb	2018-11-30

ID:: 4965564

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