GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5747593 Query DataSets for GSM5747593
Status Public on Jun 07, 2023
Title hy5hyh-FR rep3
Sample type SRA
Source name aerial tissue
Organism Arabidopsis thaliana
Characteristics treatment: FR LEDS
genotype: hy5/hyh
plant line: hy5/hyh mutant
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 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
BioSample SAMN24298413
SRA SRX13486984

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap