|
| Status |
Public on Oct 23, 2024 |
| Title |
VPNS2_1 |
| Sample type |
SRA |
| |
|
| Source name |
8099
|
| Organism |
Escherichia coli |
| Characteristics |
strain: 8099
agent: violet phosphorene nanosheets
time: 3h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAprep Pure Cell/Bacteria Kit DP430 of QIAGEN according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then 1 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. F
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Oct 23, 2024 |
| Contact name |
qiudi shen |
| E-mail(s) |
[email protected]
|
| Phone |
15247193585
|
| Organization name |
Inner Mongolia University
|
| Street address |
235 University Street West
|
| City |
Hohhot |
| ZIP/Postal code |
010000 |
| Country |
China |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE226031 |
Bacterial Elimination via Cell Membrane Penetration by Violet Phosphorene Peripheral Sub-Nanoneedles Combined with Oxidative Stress |
|
| Relations |
| BioSample |
SAMN33434738 |
| SRA |
SRX19494990 |
