|
| Status |
Public on Jul 14, 2018 |
| Title |
cop1 red rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Col-0
genotype/variation: cop1-4
tissue: Seedlings
age: 3 days
treatment: 1h red light
|
| Treatment protocol |
The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days before treated for 3 hours of white light and 21 hours of dark incubation to induce germination. After initial 24 hours, seeds were further treated with far-red light (10 µmole/s2/m2) to inactivate phytochrome activity. After additional two days in the dark, seedlings were either collected (dark sample) or treated with 1 hour of continuous red light (red sample) (8 µmole/s2/m2).
|
| Growth protocol |
Total five genotypes: Col-0, cop1-4, spaQ, phyAphyB/phyB FL, and phyAphyB/phyB ΔC plants were used for mRNA sequencing analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using sigma plant total RNA kit (Sigma, Cat.# STRN250).
NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB Cat.# E7370S) was used to generate mRNA sequencing library according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
cop1_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt
|
| Data processing |
FastQC
Bowtie2
Tophat
HTseq
DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Total_Count.txt: Tab-delimited text file includes raw counts after HTseq.
|
| |
|
| Submission date |
Jul 13, 2018 |
| Last update date |
Feb 05, 2019 |
| Contact name |
Inyup Paik |
| E-mail(s) |
inyuppaik@gmail.com
|
| Organization name |
UT Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Enamul Huq lab
|
| Street address |
NHB 2.616, Stop A5000 100 East 24th St.
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE117114 |
Phytochrome B-SPA-COP1 regulation of red light induced gene expressions in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN09655938 |
| SRA |
SRX4390353 |
