|
Status |
Public on Mar 27, 2021 |
Title |
MF41_flg22_rep2 (MAE287) |
Sample type |
SRA |
|
|
Source name |
Seedlings
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col-0 bacteria presence: MF41 treatment: flg22 time: T12 experiment: e2
|
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 |
SAMN15849593 |
SRA |
SRX8963653 |