|
| Status |
Public on Sep 08, 2019 |
| Title |
D5_SAP11aywb_NONexposed |
| Sample type |
SRA |
| |
|
| Source name |
A.thaliana leaf tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
line: SAP11 overexpressed
treatment: non treated
tag: Leaf tissue
|
| Treatment protocol |
Seven week A.thaliana old plants were exposed to M. quadrilineatus for three days. Three week Z.mays old platns were exposed to D. maidis for three days.
|
| Growth protocol |
Arabidopsis plants were grown under controlled environmental conditions with a 14h, 22 C°/ 10h, 20°C dark / light period. Zea mays plants were grown under controlled environmental conditions with 16h, 26°C/ 8h, 20°C light/dark period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ground leaf tissue using RNeasy plant mini kit
libraries were generated with the llumina Truseq strand-specific mRNA library preparation withhout size selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Arabidopsis thaliana
|
| |
|
| Submission date |
Aug 10, 2018 |
| Last update date |
Sep 08, 2019 |
| Contact name |
Archana Singh |
| E-mail(s) |
archana.bhubioinfo@gmail.com
|
| Organization name |
Cambridge University
|
| Department |
Plant Science
|
| Street address |
Downing Street
|
| City |
Cambridge |
| State/province |
England |
| ZIP/Postal code |
CB23EA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE118427 |
Phytoplasma SAP11 homologs differentially modulate development and defence in Arabidopsis and maize via destabilization of specific TCPs |
|
| Relations |
| BioSample |
SAMN09811610 |
| SRA |
SRX4547567 |
