|
| Status |
Public on May 25, 2017 |
| Title |
CK3 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: CAUH2
growth condition: OD600 ~ 0.8
treatment: untreated
|
| Treatment protocol |
Samples of H2O2-treated group were further cultrued in 5mM H2O2-contained MRS media at 37℃ for 30 min
|
| Growth protocol |
Samples of control group and H2O2-treated group were cultrued in MRS media at 37℃ until OD600 ~ 0.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested by centrifugation, flash frozen by liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw data of fastq 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 sequence of 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 FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq R package v1.18.0. DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: NC_999999999.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
|
| |
|
| Submission date |
May 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yang Yang |
| E-mail(s) |
75700656@qq.com
|
| Organization name |
China Agricultural University
|
| Department |
College of Food Science and Nutritional Engineering
|
| Street address |
No. 17 Tsing Hua East Road，HaiDian District
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL23496 |
| Series (1) |
| GSE99096 |
Global transcriptional responses to oxidative stress conditions in lactobacillus plantarum |
|
| Relations |
| BioSample |
SAMN07146601 |
| SRA |
SRX2836949 |
