|
| Status |
Public on Sep 07, 2023 |
| Title |
DRM3_3 |
| Sample type |
SRA |
| |
|
| Source name |
microbial cells
|
| Organism |
Zymomonas mobilis |
| Characteristics |
tissue: microbial cells
cell line: ZM4
cell type: whole cell
genotype: wt
treatment: grown to log phase
|
| Treatment protocol |
No special treatment was included.
|
| Growth protocol |
Cells were cultured in a standard RMG2 medium for Zymomonas mobilis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was quantified and qualified by Agilent 2100/2200 Bioanalyzer, NanoDrop and 1% agrose gel. 1μg total RNA was used for following library preparation
Generation sequencing library preparations were constructed according to the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Bcl2fastq (v2.17.1.14)
Quality assessment was performed using FastQC (v0.12.1), and based on the results, the paired FASTQ files were further subjected to quality trimming and adapter removal using Trim Galore (v0.6.10) tool.
Alignment of sequencing data was performed using hisat2(v2.2.1), followed by conversion between SAM and BAM files using samtools(v1.9)
featureCounts(v2.0.1) was used to generate counts
Performing data normalization and FPKM value conversion using the R programming language
Assembly: The reference sequence is from the Genebank database under NCBI, with the unique identifier sequence being AE008692
Supplementary files format and content: Displaying count values in matrix format
Supplementary files format and content: Displaying FPKM values in matrix format
|
| |
|
| Submission date |
Sep 07, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Wenfang Peng |
| Organization name |
Hubei University
|
| Street address |
No.368 Youyi Avenue
|
| City |
Wuhan |
| ZIP/Postal code |
420062 |
| Country |
China |
| |
|
| Platform ID |
GPL33295 |
| Series (1) |
| GSE242573 |
Gene expression analysis of Zymomonas mobilis ZM4 for promoter strengths prediction |
|
| Relations |
| BioSample |
SAMN37316355 |
| SRA |
SRX21659711 |
