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Sample GSM5074290 Query DataSets for GSM5074290
Status Public on Feb 11, 2021
Title 190RQS11
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics genotype: COL
cultivar: col-0
tissue: seedlings
photoperiod: LD(16-hour long-day)
temperature: 4C
time_post_treatment: 2.0h
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 (https://www.lexogen.com/quantseq-data-analysis/). 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
E-mail(s) wigge@igzev.de
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
Relations
BioSample SAMN17855414
SRA SRX10067438

Supplementary file Size Download File type/resource
GSM5074290_data.190RQS11.star_out.csv.gz 206.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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