GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5074285 Query DataSets for GSM5074285
Status Public on Feb 11, 2021
Title 190RQS6
Sample type SRA
Source name seedlings
Organism Arabidopsis thaliana
Characteristics genotype: COL
cultivar: col-0
tissue: seedlings
photoperiod: LD(16-hour long-day)
temperature: 22C
time_post_treatment: 0.5h
replicate: single
Growth protocol Seeds were surface-sterilised using ethanol or vapour-phase sterilisation (Clough & Bent, 1998) and stratified in respective growth media in the dark at 4˚C for 72 hours. Growth cabinets were maintained at 65% relative humidity and 170 µmol/m2/s light, unless specified otherwise, and as specified per experiment seedlings were grown at 20˚C with a 12-hour photoperiod or at 22˚C with either continuous light, a 16-hour long-day photoperiod or an 8-hour short-day photoperiod.
For gene expression analyses, SUnSET assays, seedlings were grown for 7-9 days in half-strength Murashige-Skoog liquid medium (½×MS; 0.22% w/v Murashige-Skoog mix including vitamins; M0222, Duchefa) containing 0.05% w/v MES (2-[N-morpholino]ethanesulfonic acid; 69892, Sigma), adjusted to pH 5.7 and supplemented with 0.1% w/v glucose after autoclaving (‘½MMG medium’ hereafter) (22˚C long days, with the following exceptions: 22˚C short days for Fig. 1C, and 22˚C continuous light for Figs. 2B, 3A, 3B, 4E). The seedlings were cultured in 12- or 6-well plates (657-160 and 665-180, Greiner Bio-One), with 1 mL or 2 mL of liquid medium per well, respectively, and sealed with Micropore tape. For aequorin-based calcium measurements, seedlings were grown in ½MMG for 8 to 12 days at 20˚C with a 12-hour photoperiod.
Extracted molecule total RNA
Extraction protocol For transcriptomic analyses by RNA-seq, total RNA was extracted and DNase-treated using MagMAX-96 Total RNA Isolation Kit (AM1830, Thermo Fisher Scientific). RNA was quantified using the Qubit fluorometer (Thermo Fisher Scientific) and RNA profiles were analysed using a TapeStation 2200 (Agilent) with RNA ScreenTapes (5067-5576, Agilent).
Libraries for sequencing were prepared from 500 ng RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen), according to manufacturer instructions. DNA libraries were quantified using a Qubit fluorometer, and library profiles were analysed using a TapeStation 2200 with High Sensitivity D1000 ScreenTapes (5067-5584, Agilent). Libraries were sequenced on a NextSeq-500 (Illumina; paired-end 75bp reads), according to Illumina guidelines.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Genome_build: TAIR10
Raw fastq were uploaded to Bluebee Genomics Platform and analysed with Quantseq FWD analysis pipeline ( Briefly, the raw reads were trimmed with BBDuk and aligned to GTF-annotated genome with STAR.
Supplementary_files_format_and_content: *.csv: reported by STAR, the read counts and the calculated count-per-million (CPM) values
Submission date Feb 10, 2021
Last update date Feb 11, 2021
Contact name Philip Wigge
Organization name Cambridge University
Department Sainsbury Laboratory
Street address 47 Bateman street
City Cambridge
ZIP/Postal code CB2 1LR
Country United Kingdom
Platform ID GPL19580
Series (1)
GSE166543 Ribosomes act as cryosensors in plants
BioSample SAMN17855459
SRA SRX10067433

Supplementary file Size Download File type/resource
GSM5074285_data.190RQS6.star_out.csv.gz 196.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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