|
| Status |
Public on Jun 07, 2023 |
| Title |
WS-UV rep2 |
| Sample type |
SRA |
| |
|
| Source name |
aerial tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: UV-B
genotype: Ws
plant line: Wassilewskija
|
| Treatment protocol |
Ws and hy5/hyh seedlings were grown for 7 d in continuous white light (WL) before transfer to WL, +FR, +UV-B or +FR+UV-B for 4 h.
|
| Growth protocol |
Seeds were sown directly onto a 3:1 mixture of compost and horticultural silver sand. Unless otherwise stated, seeds were stratified for 3 d in darkness at 4 °C before transfer to controlled growth cabinets (Microclima 1600E, Snijder Scientific, The Netherlands) set to 16 h light /8 h dark cycles (R:FR ~ 2.5) at 20 °C and 70% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing with the Illumina TruSeq Stranded mRNA Library Preparation Kit (Illumina, Inc., San Diego, USA)
RNA libraries were prepared following manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed with Illumina RTA 2.4.6
Reads trimmed and filtered with Trimmomatic v0.39 (SLIDINGWINDOW:5:20 MINLEN:50)
Reads were aligned against the A. thaliana TAIR10 genome assembly downloaded from plants.ensembl.org using HISAT2 v2.2.1
Gene count tables were generated with HTSeq-count v0.13.5
Differential gene expression analysis was performed using the R v4.0.3 package DESeq2 v1.30.1, using default settings
Genome_build: TAIR10: GCA_000001735.1
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample
|
| |
|
| Submission date |
Dec 22, 2021 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Keara Franklin |
| Organization name |
University of Bristol
|
| Department |
School of Biological Sciences
|
| Street address |
24 Tyndall Avenue
|
| City |
Bristol |
| ZIP/Postal code |
BS8 1TQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE192469 |
ELONGATED HYPOCOTYL (HY5) AND HY5 HOMOLOG (HYH) maintain shade avoidance suppression in sunlight |
|
| Relations |
| BioSample |
SAMN24298415 |
| SRA |
SRX13486982 |
