|
Status |
Public on Jul 08, 2012 |
Title |
Col-0 RNA-Seq replicate 2 |
Sample type |
SRA |
|
|
Source name |
Col-0 RNA-Seq
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col-0 genotype/variation: wild type tissue: etiolated 5d-old seedlings
|
Growth protocol |
Seedlings were grown on MS medium containing BRZ (brassinosteroid biosynthesis inhibitor) in the dark for 5 days before harvesting.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 5-day-old seedlings using the Spectrum Plant Total RNA kit (Sigma, USA). Libraries were constructed using TruSeqTM RNA Sample Preparation Kit (Illumina) according to the manufacturer’s procedure.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
RNA-Seq of Col-0 replicate 2
|
Data processing |
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode. Genome Build: C_L2.count.txt: Arabidopsis TAIR9
|
|
|
Submission date |
Apr 11, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Eunkyoo Oh |
Organization name |
Carnegie Institution
|
Department |
Plant Biology
|
Street address |
260 Panama Street
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL13222 |
Series (2) |
GSE37159 |
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses [RNA-seq] |
GSE37160 |
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses |
|
Relations |
SRA |
SRX140102 |
BioSample |
SAMN00854768 |