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| Status |
Public on Feb 11, 2021 |
| Title |
190RQS28 |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: COL
cultivar: col-0
tissue: seedlings
photoperiod: LD(16-hour long-day)
temperature: 22C
time_post_treatment: 6.0h
replicate: single
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Feb 10, 2021 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Philip Wigge |
| E-mail(s) |
wigge@igzev.de
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| Organization name |
Cambridge University
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| Department |
Sainsbury Laboratory
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| Street address |
47 Bateman street
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE166543 |
Ribosomes act as cryosensors in plants |
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| Relations |
| BioSample |
SAMN17855364 |
| SRA |
SRX10067455 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5074307_data.190RQS28.star_out.csv.gz |
173.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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