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| Status |
Public on Apr 24, 2022 |
| Title |
6perACSH Glucose Rep 1 |
| Sample type |
SRA |
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| Source name |
bacteria
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| Organism |
Zymomonas mobilis |
| Characteristics |
strain: Z. mobilis 2032
cell type: bacteria
treatment: 6perACSH Glucose
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Apr 21, 2022 |
| Last update date |
Apr 24, 2022 |
| Contact name |
Kevin S Myers |
| E-mail(s) |
kmyers2@wisc.edu
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| Organization name |
University of Wisconsin - Madison
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| Department |
Great Lakes Bioenergy Research Center
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| Street address |
5127 WEI, 1552 University Ave
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53726 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN27723630 |
| SRA |
SRX14953908 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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