metatranscriptome of iron microbial mat: wetland at the Savannah Rive... - SRA

SRX24792896: metatranscriptome of iron microbial mat: wetland at the Savannah River Site
1 ILLUMINA (Illumina NovaSeq X) run: 27.9M spots, 8.1G bases, 1.5Gb downloads

Design: An Illumina Low Input (RNA) library was constructed and sequenced 2x151 using the Illumina NovaSeq platform. Raw reads were processed with BBDuk (version 39.01) to remove contaminants, trim adapter sequences, remove homopolymer tails with 5 Gs, and right quality trim reads where quality drops to 0. BBDuk was also used to remove reads that contained 1 or more 'N' bases, had an average quality score below 10, or had a minimum length <51 bp. Reads mapped with BBMap to contaminants (human, cat, dog, mouse, common microbial contaminants, ribosomal RNA, or known spike-ins) were also removed

Submitted by: University of Delaware

Study: Metagenomes of iron microbial mats from a freshwater terrestrial stream and wetlands. Metagenome

PRJNA1117470 • SRP511621 • All experiments • All runs

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Our work focuses on Tims Branch at the Savannah River Site (SRS), a tributary that flowsdirectly into the Savannah River in South Carolina. Macroscopic freshwater iron mats are widespread inTims Branch; furthermore, microscopy of these mats shows biomineral morphologies consistent with theknown FeOB genera Leptothrix and Gallionella. These factors make Tims Branch ideal for studying ironoxidizers. This project is designed to fill research gaps surrounding the rate and controls on environmentaliron oxidation, and the metabolism of FeOB.The research objectives are:Objective 1: Quantify microbial iron oxidation rates in terrestrial iron mats using an integratedfield and kinetics studyObjective 2: Identify and quantify dominant iron-oxidizing microorganisms in terrestrialiron mats using metagenomics and metatranscriptomicsObjective 3: Construct microbial metabolic models of iron oxidizers and iron matcommunities to link microbial iron oxidation to C, N and S cycling

Sample:

SAMN41570321 • SRS21510023 • All experiments • All runs

Organism: microbial mat metagenome

Library:

Name: 2201MN3_MT

Instrument: Illumina NovaSeq X

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: other

Layout: PAIRED

Runs: 1 run, 27.9M spots, 8.1G bases, 1.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR29275561	27,857,305	8.1G	1.5Gb	2024-07-26

ID:: 33118234

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