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Sample GSM4159021 Query DataSets for GSM4159021
Status Public on Oct 02, 2020
Title DMSO 1 h agb13
Sample type SRA
 
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics ecotype/background: Col-0
genotype/variation: agb1
tissue: Seedlings
treatment: DMSO
treatment time: 1 h
age: 4 days
Treatment protocol After four days, the seedlings were separated into groups of 515 using sterile toothpicks and moved to 20 mL of ½ Murashige and Skoog in a petri dish (100 x 25 mm, Fisher Scientific). The seedlings were treated with 0.2% DMSO (Sigma-Aldrich), 40 µM NAE 18:3 (Cayman Chemical) for 1 h or 3 h. After 1 h or 3h, whole seedlings were collected from each treatment group, flash frozen, and stored at -80°C.
Growth protocol Arabidopsis seeds were surface sterilized by treatment with 70% ethanol for 3 min followed by 20% bleach (5.25 % sodium hypochlorite, Clorox) with 0.01% Triton X-100 (Sigma-Aldrich) for 5 min and then rinsed five times with sterile ddH2O. After the final rinse, Arabidopsis seeds were maintained in 1 mL of sterile ddH2O, wrapped in two layers of aluminum foil, and placed in the dark at 4°C for three days. After three days, the seedlings were sown in 50 mL of ½ Murashige and Skoog (Sigma-Aldrich) media, pH 5.7 with 1% sucrose (Fisher Scientific) in a 250 mL sterile Erlenmeyer flask. The seeds were grown at 21°C, 80 -110 µmoles/m2s, on a shaker (Bellco Biotechnologies) set at speed level 3.
Extracted molecule total RNA
Extraction protocol Each Arabidopsis seedling sample was ground to a fine powder and 500 µL of Hot Borate Buffer (200mM sodium tetraborate decahydrate - Sigma-Aldrich, 30 mM EGTA - Sigma-Aldrich, 1% SDS - Fisher, 1% deoxycholic acid - Sigma-Aldrich, 2% polyvinylpyrrolidone (PVP) 40K - Sigma-Aldrich, 0.5% IGEPAL CA-630 - Sigma-Aldrich, 10 mM DTT - Sigma-Aldrich) and 17.5 µL of 20 mg/mL Proteinase K (ThermoFisher) were added. After mixing, the sample and buffer solution were added to a lilac shredder column from a RNeasy Plant Mini Kit (Qiagen). The manufacturer's protocol from the RNeasy Plant Mini Kit was followed for the remainder of the extraction.
Poly(A) enrichment and library preparation were performed using the TruSeq Stranded mRNA prep kit (Illumina). Libraries were quantified by fluorometry, immobilized, and processed onto a flow cell, followed by 2 x 75 bp sequencing-by-synthesis on a Next-Seq 500 system (Illumina) with two mid-output cassettes (Illumina). Library construction and RNA sequencing were performed by the UNT Genomics Center (http://untgenomicscenter.squarespace.com/).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 1hbeta_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv
Data processing Reads were mapped to the reference using STAR and the default settings.
Expression analysis was completed using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: "counttable.txt" files are output from STAR.
Supplementary_files_format_and_content: "normalized_countstable.csv" files are output normalized counts from DESeq2.
 
Submission date Nov 12, 2019
Last update date Oct 02, 2020
Contact name Ashley Elisabeth Cannon
E-mail(s) ashley.cannon@unt.edu
Organization name The University of North Texas
Department Biological Sciences
Lab Chapman
Street address 1155 Union Circle #305220
City Denton
State/province TX
ZIP/Postal code 76203-5017
Country USA
 
Platform ID GPL19580
Series (1)
GSE140294 An intact heterotrimeric G-Protein complex is required for the N-acylethanolamine-induced, transcriptionally-mediated chloroplast response in developing Arabidopsis seedlings
Relations
BioSample SAMN13266900
SRA SRX7131247

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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