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Sample GSM6876609 Query DataSets for GSM6876609
Status Public on May 16, 2024
Title ZM532, AF, rna-seq, rep1
Sample type SRA
 
Source name ZM532
Organism Zymomonas mobilis
Characteristics strain: ZM532
genotype: Genomic mutants
treatment: Acetic acid and furfural
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the trizol method and checked on an agarose gel to monitor the degradation and contamination. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent).
Sequencing libraries were generated from 1 μg total RNA per sample using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing The raw sequencing data was first subjected to quality control using FraserQC (v1.2) with the default parameters.
Reads were then aligned to Z. mobilis ZM4 reference genome using Bowtie2.
Genes expression levels were quantified by featureCounts of Subread package.
Differentially expressed genes (DEGs) were screened according to the criteria of Foldchange ≥ 2 and FDR < 0.05 by DESeq2. GO enrichment of DEGs was analyzed by clusterProfiler.
Assembly: NC_006526.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
 
Submission date Dec 21, 2022
Last update date May 16, 2024
Contact name Mao Chen
E-mail(s) chenmao92@hotmail.com
Organization name Biogas Institute of Ministry of Agriculture and Rural Affairs
Street address Section 4-13, Renmin Rd. South
City Chengdu
ZIP/Postal code 610041
Country China
 
Platform ID GPL32966
Series (2)
GSE221498 Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation [RNA-Seq]
GSE221499 Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation
Relations
BioSample SAMN32347309
SRA SRX18804546

Supplementary file Size Download File type/resource
GSM6876609_ZM532_RM_FPKM_R1.txt.gz 56.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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