|
| Status |
Public on Jan 11, 2018 |
| Title |
srt1srt2 4 hour ethylene RNAseq, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
srt1srt2 4 hour ethylene RNAseq
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col
genotype/variation: srt1srt2 mutant
age: 3-day
tissue: 3-day old etiolated seedlings
treated with: ethylene for 4 hours
|
| Treatment protocol |
Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million (ppm) ethylene) for 4 hours
|
| Growth protocol |
Arabidopsis seeds were dark-grown and treated with air (hydrocarbon-free air (Zero grade air, AirGas)) at 24 ºC for 3 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ethylene treated for 4 hours
|
| Data processing |
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using TopHat version 2.0.9 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.2.1
Genome_build: tair10
Supplementary_files_format_and_content: srt1srt2_arivsC2H4.xlsx file include RPKM values for each Sample, generated by Cuffdiff version 2.2.1
|
| |
|
| Submission date |
Jul 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
FAN ZHANG |
| E-mail(s) |
biozhangfancn@outlook.com
|
| Organization name |
The University of Texas at Austin
|
| Street address |
2506 speedway, NMS5.324
|
| City |
Austin |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE101762 |
Histone deacetylase SRT2 mediates ethylene-induced transcriptional repression through interaction with ENAP1 |
|
| Relations |
| BioSample |
SAMN07376156 |
| SRA |
SRX3028008 |
