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Sample GSM5172109

Query DataSets for GSM5172109

Status

Public on May 10, 2023

Title

RM532_3

Sample type

SRA

Source name

ZM532

Organism

Zymomonas mobilis

Characteristics

strain: ZM532
treatment: Acetic acid and furfural
medium: RM

Extracted molecule

total RNA

Extraction protocol

Total RNAs were extracted using the RNA isolation kit from bacteria cells (2 strains × 2 conditions × 3 replications) cultured in RM and AF medium (Tiangen, China).
Highly qualified RNAs were used for construction and sequencing of cDNA libraries. The high-throughput sequencing was conducted by Illumina Hiseq 2000 platform after passing via a number of screening phases

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Raw data (raw reads) were interpreted via in-house perl scripts and clean data was extracted by eliminating reads comprising adapters. Then, the clean data of Q20, Q30, and GC content were computed. Complete genome annotation files downloaded from the genome website Bowtie2-2.2.3 (ftp://ftp.ncbi.nlm.nih.gov/genomes/bacteria/Zymomonas_mobilis/) were used to construct a reference genome index and match clean reads to the reference genome [33]. Novel genes, operon and transcription start sites were identified by Rockhopper [22]. Then, extracted the 5’UTR (3’UTR) sequences. Then, RBS finder [34] and TransTermHP ([35] were used to predict SD sequences and terminator sequences, respectively. IntaRNA was used to predict the sRNA targets. And then we used RNAfold to predict RNA secondary structures [36, 37]. Mapping of clean reads to each gene was counted using HTSeq v0.6.1. The fragments per kilobase of exon per million fragments mapped (FPKM) reads of every single gene were determined as described earlie
The read counts were modified for each sequenced library by edger software package via one standardized scaling factor. Differentially expression genes (DEGs) analyses of two conditions were performed using the DESeq package in R (1.18.0) [39]. Then using Benjamini & Hochberg approach, the p-values were adjusted. Genes with fold change (FC) > 1.5 and a false discovery rate (FDR; < 0.05) were considered as DEGs. Gene Ontology (GO) and pathway enrichment analyses of the DEGs were implemented with GOseq package in R [40], respectively. GO terminologies with adjusted p-value less than 0.05 were identified as significantly enriched.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm.stat.xls: a statistical table of the number of genes in different expression level intervals, this table counts the number of genes at different expression levels and the expression level of a single gene
Supplementary_files_format_and_content: New transcript annotation results

Submission date

Mar 15, 2021

Last update date

May 10, 2023

Contact name

Samina Shabbir

E-mail(s)

samishabbir90@gmail.com

Organization name

Graduate School of Chinese Academy of Agricultural Science,

Department

Biomass Energy Technology Research Centre