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Sample GSM8439682 Query DataSets for GSM8439682
Status Public on Jan 16, 2025
Title Arabidopsis, leaf, well-watered, undigested, rep1
Sample type SRA
 
Source name Third true leaf at 14 days after stratification
Organism Arabidopsis thaliana
Characteristics tissue: Third true leaf at 14 days after stratification
cell type: Whole leaf, undigested
genotype: Col-0
treatment: Well-watered
Treatment protocol Per condition and per biological replicate, 5-6 third true leaves were pooled and immediatly frozen in liquid nitrogen for the "Undigested leaf" samples. For the digested samples (either without ("digested") or with fixation("fixed, digested")), ~80 third true leaves were harvested with a tweezer and pooled for tissue digestion by cell wall degradation. Tissue digestion protocol was adapted from (Ryu et al., 2019). The tissue was chopped and incubated in 1 ml cell wall digestion solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES, 20 mM KCl, 2% (wt/vol) cellulase and 0.5% (wt/vol) macero enzyme) and subsequently transferred to a 70-μm cell strainer placed in a 6-well plate. Extra cell wall digestion solution was added up to 5 ml. For the samples in which transcription had to be inhibited, Actinomycin D (ActD) was added to a concentration of 35 μM. Cell wall digestion was done by constantly shaking for 75 min at room temperature. After a 7-min centrifugation at 100 g, the pellet was resuspended in 1 ml washing solution (0.4 M mannitol, 10 mM CaCl2, 20 mM MES and 20 mM KCl).
Growth protocol Arabidopsis Col-0 was grown under a long-day regime (intensity 110–120 μmol m−2s−1) at 21 °C on the WIWAM platform (http://www.wiwam.be). Five seedlings were grown per pot in order to obtain 80 seedlings per conditions (well-watered or mild drought, see later), per biological replicate. The seeds were sown in 85±1 g of Saniflor compost (Van Isreal N.V., Geraardsbergen, Belgium) with an average absolute water content of 70%. Plants were watered daily until 8 days after stratification (DAS) with a well‐watered regime of soil relative water content (RWC) 69% (2.2 gwater/gsoil). At 9 DAS, half of the pots (randomized) were not watered (MD) until harvest (14 DAS) while the other half kept the well-watered (WW) regime. The biological replicates were harvested as follows: a first experiment was performed to generate all "Rep1" samples and a second, fully independent experiment was performed six months later. All "Rep2" and "Rep3" samples were harvested from that experiment, from independently treated pots.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the ReliaPrep RNA extraction kit (Promega) according to the manufacturer’s instructions.
All samples were further processed by BGI TECH SOLUTIONS (Poland), where the RNA integrity was verified prior to library preparation. The library was sequenced on the DNBseq platform, and around 30M 150 bp pair-end reads were aimed for. After initial filtering by BGI, the number of reads retrieved for each sample was around 20M.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description Rep1_ww_undigested
Data processing The data was processed using Galaxy. Reads were mapped on the Arabidopsis genome (TAIR 10) using the RNA-seq aligner tool STAR (Dobin et al., 2013). Statistical analysis was performed using the DESEQ package (Anders and Huber, 2010).
Assembly: TAIR10
Supplementary files format and content: The Excel file contains the normalized counts for each sample.
 
Submission date Aug 04, 2024
Last update date Jan 16, 2025
Contact name Marieke Dubois
E-mail(s) marieke.dubois@psb.vib-ugent.be
Phone 0475337819
Organization name PSB, Vlaams Instituut voor Biotechnologie (VIB)
Street address Technologiepark 71
City Gent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL28290
Series (1)
GSE273926 Dual and spatially resolved drought responses in the Arabidopsis leaf mesophyll revealed by single-cell transcriptomics
Relations
BioSample SAMN43025196
SRA SRX25595394

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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