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| Status |
Public on Oct 02, 2020 |
| Title |
NAE 18:3 1 h agb13 |
| Sample type |
SRA |
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| Source name |
Seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Col-0
genotype/variation: agb1
tissue: Seedlings
treatment: NAE 18:3
treatment time: 1 h
age: 4 days
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| 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.
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| 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.
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| 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/).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
1hbeta183_3
processed data file: 1h_countdata.txt
processed data file: 1h_normalized_countstable.csv
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| 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.
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| Submission date |
Nov 12, 2019 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Ashley Elisabeth Cannon |
| E-mail(s) |
ashley.cannon@unt.edu
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| Organization name |
The University of North Texas
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| Department |
Biological Sciences
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| Lab |
Chapman
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| Street address |
1155 Union Circle #305220
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| City |
Denton |
| State/province |
TX |
| ZIP/Postal code |
76203-5017 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN13266897 |
| SRA |
SRX7131250 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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