|
| Status |
Public on Dec 18, 2012 |
| Title |
BP12-2 seedling treated with rapamycin_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype/variation: BP12-2
treatment: 10 µg/ml rapamycin
|
| Treatment protocol |
WT and BP12-2 seedlings at 15 DAG were treated with rapamycin for 3 days by transferring them from 0.5MS medium to 0.5 MS+10 µg/ml rapamycin along with control (0.5 MS +1µl/ml DMSO)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA were isolated from the samples by using RNeasy plant mini kit (QIAGEN, cat. no. 74904) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired-end alignments were obtained through aligning short reads onto the reference Arabidopsis Genome (TAIR9) using Bowtie. More than 80% of the reads mapped onto the genome.
Htseq-count was used to count the reads from the Bowtie derived output files.
Differential expressed genes were identified using edgeR. The FDR-corrected P value for differential expression was set to be ≤0.05.
Genome_build: Arabidopsis Genome (TAIR9)
|
| |
|
| Submission date |
Dec 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Raju Datla |
| E-mail(s) |
raju.datla@nrc-cnrc.gc.ca
|
| Phone |
306-975-5267
|
| Organization name |
National Research Council
|
| Department |
Plant Biotechnology Institute
|
| Street address |
110 Gymnasium Place
|
| City |
Saskatoon |
| State/province |
SK |
| ZIP/Postal code |
S7N 0W9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE42968 |
Differentially regulated genes in TOR knockdown Arabidopsis lines |
|
| Relations |
| SRA |
SRX210993 |
| BioSample |
SAMN01831502 |
