|
| Status |
Public on Dec 31, 2017 |
| Title |
phyB-9.D100h.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
transgenic-line: phyB-9
replicate: 1
|
| Treatment protocol |
Seedlings were grown for 100h in the dark, and harvested under dim green light using liquid nitrogen.
|
| Growth protocol |
Arabidopsis thaliana seeds were stratified for 5 days at 4 degree celcius in the dark, followed by a 3h far-red light (10 µmol m-2 s-1) treatment and then wrapped in the dark for another 97h in a growth chamber maintained at 21 degree celcius.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
100 mg 100h dark-grown seedlings were collected under dim green light, flash frozen in liquid nitrogen, and total RNA was extracted using Zymo Quick-RNA™ MiniPrep (R1055).
RNA libraries were prepared for sequencing using the standard protocol of NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (#E7420S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Null mutant of Arabidopsis PHYB, Col-0 background
|
| Data processing |
Illumina Casava1.7 software used for basecalling??
Sequenced reads were de-multicomplexed according to the barcodes.
Paired-end reads were mapped to the Arabidopsis TAIR10 genome and transcriptome using Tophat/v2.0.14 (Kim et al., 2013).
Gene expression was estimated using Cufflinks/v2.2.1 (Trapnell, Williams et al. 2010), and then differential gene expression between BCY and phyB-9 was determined by Cuffdiff/v2.2.1 (Trapnell, Hendrickson et al. 2013) using a q-value cutoff of 0.05 and a fold-change equal to or greater than 1.5. Since the RNA-seq libraries were constructed using the NEBNext Ultra Directional RNA library prep kit for Illumina and preserved information about the RNA strand orientation, the tophat and cufflinks parameter “--library-type fr-firststrand” was used to distinguish sense reads and anti-sense reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited gene_exp.diff txt file generated by cuffdiff software. The file contains differential gene expression FPKM values between BCY and phyB-9.
|
| |
|
| Submission date |
Dec 06, 2016 |
| Last update date |
Jul 25, 2024 |
| Contact name |
Meng Chen |
| E-mail(s) |
meng.chen@ucr.edu
|
| Phone |
9518275635
|
| Organization name |
University of California, Riverside
|
| Street address |
2150 Batchelor Hall, 900 University Ave.
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE90925 |
Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B |
|
| Relations |
| BioSample |
SAMN06112622 |
| SRA |
SRX2398181 |
