|
| Status |
Public on Mar 27, 2021 |
| Title |
MF138_Mock_rep2 (MAE086) |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
bacteria presence: MF138
treatment: Mock
time: T12
experiment: e1
|
| Treatment protocol |
Seven-day old seedlings were transferred to Johnson medium with or without 1 µM of flg22 (in the presence of a commensal strain; 10e5 cfu/mL). Plates were kept in a growth chamber under a 9-hour light/15-hour dark regime at 21oC day/18oC night. The entire eedlings was harvested for RNA extraction 12 days after the transfer to the treatment plates.
|
| Growth protocol |
Arabidopsis seeds were germinated on Johnson medium solidified with 1% bacto-agar. Plates were kept in the vertical position for seven days in a growth chamber under a 16-hour light/8-hour dark regime at 21oC day/18oC night. The resulting seedlings were then submitted to the treatments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample
|
| |
|
| Submission date |
Aug 18, 2020 |
| Last update date |
Mar 27, 2021 |
| Contact name |
Paulo Teixeira |
| E-mail(s) |
paulojt@usp.br
|
| Phone |
+551934294344
|
| Organization name |
University of São Paulo (ESALQ/USP)
|
| Department |
Biology
|
| Street address |
Av. Pádua Dias, 11
|
| City |
Piracicaba |
| State/province |
SP |
| ZIP/Postal code |
13418-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE156424 |
RNA-seq of Arabidopsis thaliana seedlings exposed to the MAMP flg22 in the presence of individual commensal bacteria [MAE] |
| GSE156426 |
RNA-seq of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of commensal bacteria |
|
| Relations |
| BioSample |
SAMN15849743 |
| SRA |
SRX8964095 |
