|
| Status |
Public on May 16, 2024 |
| Title |
zur, KO, RM, rna-seq, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
zur_KO
|
| Organism |
Zymomonas mobilis |
| Characteristics |
strain: zur_KO
genotype: zur knockout
treatment: RM
|
| 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 |
SAMN32347305 |
| SRA |
SRX18804550 |
