|
| Status |
Public on Feb 03, 2017 |
| Title |
RNAseq_EtOH_12h_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession: Col-0
age: 3 day
light condition: dark
treatment: EtOH mock treatment, 12 hours
|
| Treatment protocol |
10 uM ABA treatment or ethanol mock treatment for 1 to 60 hours.
|
| Growth protocol |
Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Plant RNeasy mini Kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit and sequenced by Illumina HiSeq 2500 according to the manufacturers' instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base-calling were performed by Illumina Real-Time Analysis software v1.17.20 to v1.18.61.
Sequencing reads were mapped to Arabidopsis TAIR10 genome assembly by tophat2.0.8 using default settings. Mapped reads with of mapping score equal to or larger than 10 were counted by HTSeq (v0.5.4) and analyzed by edgeR (v3.6.2) to identify differentially expressed genes using contrasts between ABA- and mock-treated samples at each time point and false discovery rate 0.01 or 0.05 as thresholds.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE80565 |
RNA-seq of abscisic acid-reponsive transcription factors |
| GSE80568 |
ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors |
|
| Relations |
| BioSample |
SAMN04884910 |
| SRA |
SRX1719942 |
