|
| Status |
Public on Apr 21, 2014 |
| Title |
infected NIK 10 days rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
NIK_infected10
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: NIK
infection: infected with CaLCuV
time: 10 dpi
tissue: leaves
|
| Treatment protocol |
The Columbia (Col-0) ecotype of Arabidopsis thaliana was used as the wild-type control, and the nik1 knockout line was used for plant transformation. A. thaliana plants at the seven-leaf stage were inoculated with plasmids containing partial tandem repeats of CaLCuV DNA-A and DNA-B by biolistic delivery
|
| Growth protocol |
The seeds were surface sterilized and cold treated at 4 °C for 2 days in the dark and then exposed to white light. The seedlings were grown at 22 °C on Murashige-Skoog medium for 3 weeks and then transferred to soil. The plants were grown in a growth chamber at 22 °C under long-day conditions (16 h light/8 h dark).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The transgenic and wild-type lines were infected at the seven-leaf stage with CaLCuV. After 10 days post-inoculation (dpi) or after 21 dpi, total RNA from systemically infected leaves, as diagnosed by PCR, and mock-inoculated leaves from wild-type, 35S::NIK1-5 and 35S::T474D-4 lines was isolated using TRIzol (Invitrogen)
RNA pair-ended libraries were prepared by the Illumina HiSeq 2000 standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava 1.8 software used for basecalling. The reads were filtered using the average of 20 phred quality.
Then the reads were mappped using arabidopsis transcriptome (cDNA) file with the Bowtie 2.1.0 aligner. The parameters for bowtie2 --very-sensitive --no-discordant --no-mixed -p 8 -5 10 -3 10 -1
A posterior alignment filter was performed by samtools samtools view -f 1 -F 12 -q 20
The normalization and differential expression analysis were performed by using the R/Bioconductor edgeR package. The normalization was the TMM factor implemented in this package.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized data in csv tables
|
| |
|
| Submission date |
Apr 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Otavio Jose Bernardes Brustolini |
| E-mail(s) |
otaviojbbrustolini@gmail.com
|
| Phone |
+553138992969
|
| Organization name |
Universidade Federal de Viçosa
|
| Department |
Bioquimica e Biologia Molecular
|
| Lab |
Biologica Molecular de Plantas
|
| Street address |
Av. PHRolfs, S/N
|
| City |
Viçosa |
| State/province |
MG |
| ZIP/Postal code |
36570000 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE56922 |
Global variation of gene expression induced by constitutive activation of the NIK receptor in Arabidopsis |
|
| Relations |
| BioSample |
SAMN02730138 |
| SRA |
SRX522624 |
