Transcriptome analisys of a diverse microbial sugar cane bagasse comp... - SRA

SRX3102815: Transcriptome analisys of a diverse microbial sugar cane bagasse composting community - Week 4
1 ILLUMINA (Illumina MiSeq) run: 5.9M spots, 2.4G bases, 1.4Gb downloads

Design: The nucleic acid extracted was diluted to 200 ng/_L and treated with DNase I (Invitrogen, Waltham, MA, USA) according to manufacturerÕs recommendation. Equimolar volumes of the extracted RNA from biological replicates were combined and the Prokaryotic ribosomal RNA (rRNA) was depleted with RiboZero Magnetic Kit Bacteria (Epicentre). The remaining RNA was purified using the RNA Clean & Concentrator-5 kit (ZymoResearch, Irvine, CA, USA). TruSeq Stranded Total RNA Sample Preparation kit (Illumina, San Diego, CA, USA) was used to deplete Eukaryotic rRNA and to synthesize a ~450 bp cDNA library. Sequencing of each time-point cDNA library was performed on a MiSeq with a 500-cycles Reagent kit v2 (Illumina, San Diego, CA, USA).

Submitted by: Universidade de Sao Paulo

Study: Transcriptome analisys of a diverse microbial sugar cane bagasse composting community

PRJNA398086 • SRP115687 • All experiments • All runs

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In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse (SCB) as the sole carbon source. Analysis of metatranscriptomic data led to the selection and functional characterisation of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme (CAZy) family 11 (GH11) with exo-1,4-ß-xylanase activity.

Sample: Week 4 of composting microbial community growing with sugarcane bagasse as carbon source

SAMN07501595 • SRS2438503 • All experiments • All runs

Organism: compost metagenome

Library:

Name: growth_SCB_week4

Instrument: Illumina MiSeq

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 5.9M spots, 2.4G bases, 1.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR5944346	5,879,612	2.4G	1.4Gb	2017-09-03

ID:: 4392674

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