|
| Status |
Public on Jun 01, 2018 |
| Title |
Atg3bp1_hrcC_2 |
| Sample type |
SRA |
| |
|
| Source name |
14 day old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: Whole seedlings
treatment: PstDC3000 hrcC-
genotype/variation: Atg3bp1 mutant
ecotype: Columbia-0
|
| Treatment protocol |
Plants were treated with Pst DC3000 hrcC- for 24 hours
|
| Growth protocol |
Plants were grown on sterile one-half-strength Murashige and Skoog (MS) medium with a 16-8h photoperiod for 14 days at 21° C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using NucleoSpin® Plant RNA kit and First-strand complementary DNA was synthesized from 1 μg of total RNA using reverse transcriptase, SuperScript® III First-Strand Synthesis SuperMix kit (Invitrogen).
Libraries were prepared using Illumina TruSeq stranded mRNA kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Atg3bp1_fpkm.txt
|
| Data processing |
Sequenced reads were checked for quality.
Low quality reads were trimed using trimmomatic.
Trimmed reads were mapped to TAIR10 genome using TOPHAT.
FPKM was calculated using cufflinks.
Differential analysis was performed using cuffdiff.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt, FPKM values
|
| |
|
| Submission date |
Dec 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Naganand Rayapuram |
| E-mail(s) |
naganand.rayapuram@kaust.edu.sa
|
| Organization name |
KAUST
|
| Street address |
KAUST
|
| City |
Thuwal |
| ZIP/Postal code |
23955 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE107786 |
The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and aploplastic immunity |
|
| Relations |
| BioSample |
SAMN08141574 |
| SRA |
SRX3452749 |
