|
Status |
Public on Jun 07, 2023 |
Title |
WS-FR rep3 |
Sample type |
SRA |
|
|
Source name |
aerial tissue
|
Organism |
Arabidopsis thaliana |
Characteristics |
treatment: FR LEDs/ 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
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|
|
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
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|
|
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 |
SAMN24298412 |
SRA |
SRX13486985 |