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Sample GSM6053154 Query DataSets for GSM6053154
Status Public on Apr 24, 2022
Title 6perACSH Xylose Rep 1
Sample type SRA
 
Source name bacteria
Organism Zymomonas mobilis
Characteristics strain: Z. mobilis 2032
cell type: bacteria
treatment: 6perACSH Xylose
Treatment protocol Samples for RNA-seq were collected by mixing 10 mL of culture with 1.25 mL ice-cold unbuffered phenol and ethanol mixture (5:95, vol/vol) as described in chwalbach, M.S., et al., Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol, 2012. 78(9): p. 3442-57.
Growth protocol Z. mobilis was grown in bioreactors as described in Yang, S., et al., Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032. Biotechnol Biofuels, 2018. 11: p. 125.
Extracted molecule total RNA
Extraction protocol RNA was extracted from cultures using a phenol-chloroform method as described in Rhodius, V.A. and C.A. Gross, Using DNA microarrays to assay part function. Methods Enzymol, 2011. 497: p. 75-113.
Illumina Low Input RNASeq w/rRNA Depletion: rRNA was removed from 100 ng of total RNA using Ribo-Zero rRNA Removal Kit (Illumina). Stranded cDNA libraries were generated using the Illumina Truseq Stranded mRNA Library Prep kit. The rRNA depleted RNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v4, and Illumina’s cBot instrument to generate a clustered flow cell for sequencing. Sequencing of the flow cell was performed on the Illumina HiSeq 2500 sequencer using HiSeq TruSeq SBS sequencing kits, v4, following a 2x100 indexed run recipe.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing For RNA-seq analysis, the paired-end FASTQ files were were trimmed using Trimmomatic version 0.3 with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming the reads were aligned to the Z. mobilis (ZM4, 8b) genome using BWA-mem version 0.7.12-r1039 with default settings. Aligned reads were mapped to gene locations using HTSeq version 0.6.0 using default settings. Raw sequencing reads were normalized using the reads per kilobase per million mapped reads (RPKM).
Assembly: GCA_003052025.1
Supplementary files format and content: Zhang_RPKM_data.txt - RPKM normalized read count values from RNA-seq, linear format
Supplementary files format and content: Zhang_RawCounts_data.txt - Raw read count values from RNA-seq, linear format
 
Submission date Apr 21, 2022
Last update date May 26, 2022
Contact name Kevin S Myers
E-mail(s) kmyers2@wisc.edu
Organization name University of Wisconsin - Madison
Department Great Lakes Bioenergy Research Center
Street address 5127 WEI, 1552 University Ave
City Madison
State/province WI
ZIP/Postal code 53726
Country USA
 
Platform ID GPL29852
Series (1)
GSE201229 Multistage  Transcriptomics Data Set of Zymomonas mobilis 2032 During Fermentation in 6% and 9% Glucan-Loading AFEX-Pretreated Corn Stover Hydrolysates and 7% Glucan-Loading AFEX-Pretreated Switchgrass Hydrolysate
Relations
BioSample SAMN27723625
SRA SRX14953913

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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