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Sample GSM8273564

Query DataSets for GSM8273564

Status

Public on May 21, 2024

Title

E. coli strain A, control strain, rep 1

Sample type

SRA

Source name

bacteria

Organism

Escherichia coli str. K-12 substr. MG1655

Characteristics

cell type: bacteria

Treatment protocol

Cells were harvested after 12 h of IPTG induction by quick centrifugation at 4℃, 12,000 rpm for 1 min, and immediately frozen in liquid nitrogen.

Growth protocol

The A (CF) and AP (pcnBi) strains were cultivated in modified M9 medium at 30℃ and inducted by IPTG when OD600 reached about 1.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the RiboPure™ Bacteria Kit (Invitrogen, USA) following the manufacturer’s recommendations. RNA quality was checked using the DNF-471 Standard Sensitivity RNA Analysis Kit (Agilent, USA) and running on Fragment Analyzer (Agilent, USA). RNA sample was treated with DNase-I to remove DNA and was subjected to TIANSeq rRNA Depletion Kit (G- Bacteria) (TIANGEN, China) to remove rRNA.
Sequencing libraries were constructed using the Optimal Dual-mode mRNA Library Prep Kit (BGI, China) following the manufacturer’s instructions. Circularization was performed using the MGIEasy Circularization Kit (MGI, China) and the product was quantitated using the Qubit® ssDNA Assay Kit (Invitrogen, USA). The libraries were then prepared using the MGISEQ-2000RS High-throughput Sequencing Set (FCL PE100) (MGI, China) and sequenced via the DNBSEQ-G400 platform (BGI, China) according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

DNBSEQ-G400

Data processing

The sequencing data was filtered with SOAPnuke (v1.5.6) by removing reads containing sequencing adapter, reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20% and reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). HISAT2 (v2.1.0) was applied to align the clean reads to the reference genome. Bowtie2 (v2.3.4.3) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1). Essentially, differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value <= 0.05. KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value <= 0.05).
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: Excel file-gene expression (fpkm, read, log2 fold change, and q-value)

Submission date

May 16, 2024

Last update date

May 21, 2024

Contact name

Lixia Fang

E-mail(s)

lxfang@tju.edu.cn

Organization name

Tianjin University

Street address

135 Yaguan Road, Jinnan District