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Sample GSM5745873 Query DataSets for GSM5745873
Status Public on Feb 24, 2022
Title Col0_4h_A
Sample type SRA
Source name Col0 4h after ABA spray replicate A
Organism Arabidopsis thaliana
Characteristics genotype: wild type
developmental stage: 12 days
tissue: Whole seedling
treatment: Abscisic acid, 10 micromole, 4h
Treatment protocol seedling were spray with a solution of 10µM of ABA dilluted in water.
Growth protocol Media = MS/2, pH 5.8, 1% Surose hygrometry = 33% humidity Temperature = 24°C day/ 21°c night Light = 16 hours day / 8 hours night for 12 days.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRI Reagent (Sigma-Aldrich) and treated with DNase (Fermentas) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.7.2a)
Reads were counted on each Araport11 features using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample
Submission date Dec 21, 2021
Last update date Feb 24, 2022
Contact name Thomas Blein
Organization name CNRS
Lab IPS2
Street address rue de Noetzlin
City Gif-sur-Yvette
ZIP/Postal code 91190
Country France
Platform ID GPL19580
Series (1)
GSE192382 Influence of the downregulation of the MARS lncRNA (AT5G00580) of the response to Abscisic acid (ABA) in Arabidopsis
BioSample SAMN24280647
SRA SRX13473100

Supplementary file Size Download File type/resource
GSM5745873_Col_t4h_A_counts.txt.gz 239.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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