|
| Status |
Public on Sep 20, 2021 |
| Title |
Arab-4G-R4-2 |
| Sample type |
SRA |
| |
|
| Source name |
16S amplicon sequencing of Arabidopsis plants root microbiome sample UGT84A3 mutant
|
| Organism |
root metagenome |
| Characteristics |
genotype/variation: UGT84A3 mutant
growth condition: grown in natural soil
|
| Treatment protocol |
Grow until mid-log phase in KB and transfer to minimal medium with the presence of indicated drugs
|
| Growth protocol |
MM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Psph strains were grown, harvested and washed as above, then the bacteria were transferred to MM at 28 ℃ for 6 hours. Total RNA was extracted by using RNeasy Mini Kit (QIAGEN, USA). Genomic DNA was removed by using DNaseI (NEB, USA) for 30 min.
After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA), which was then sequenced using the HiSeq 2000 system (Illumina, USA). All RNA-seq samples have two biological replications.
NEBNext UltraTM II RNA Library Prep Kit protocol (NEB, USA)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: otu_table_tax.txt
|
| Data processing |
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using TopHat (version 2.1.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cufflinks（version 2.2.0）.
Raw data were processed using the QIIME (v1.7.0) to get the OUT table.USEARCH software (v8.0.1) were used to generated the OUT table file by aligning the original reads back to the OTUs.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: txt files were generated from RNA-seq/root metagenome
|
| |
|
| Submission date |
Oct 30, 2020 |
| Last update date |
Sep 20, 2021 |
| Contact name |
Xin DENG |
| E-mail(s) |
[email protected]
|
| Phone |
852-34425693
|
| Organization name |
City University of Hong Kong
|
| Department |
Department of Biomedical Sciences
|
| Lab |
Dr Xin DENG's Lab
|
| Street address |
1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL29322 |
| Series (1) |
| GSE160492 |
RNA-seq for polyphenols treated Pseudomonas syringae |
|
| Relations |
| BioSample |
SAMN16605494 |
| SRA |
SRX9405670 |
