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Sample GSM5195660 Query DataSets for GSM5195660
Status Public on Apr 01, 2022
Title fbw2_1 (AGO1-IP RNA)
Sample type SRA
 
Source name AGO1-IP RNA
Organism Arabidopsis thaliana
Characteristics tissue: Seedlings
ecotype: Columbia 0
replicate: 1
genotype: fbw2
Treatment protocol No treatment
Growth protocol Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h-light/8h-dark (20,5/17°C, 70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965).
Extracted molecule total RNA
Extraction protocol RNA was extracted in Tri-Reagent according to the manufacturer’s protocol, and aqueous phase was left in 1 volume of isopropanol over-night at -20°C, precipitated 30 minutes at 16000g (4°C). Pellets were rinsed in 1 ml 70% ethanol and centrifuged an additional 10 minutes. For AGO1-loaded small RNA samples, IPs were performed as described above from 500mg of 1-week-old Arabidopsis seedlings grown on MS-agar plates. AGO1-loaded small RNA were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was then performed according to the manufacturer’s instructions.
Small RNA libraries were constructed using Real-Seq-AC kit (RealSeq®-AC, USA) according to manufacturer’s instructions with 500ng as starting material. Libraries were sequenced using Illumina Next-Seq 500 technology at University of Delaware (Delaware, USA).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model NextSeq 550
 
Data processing We trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 34-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 blastsets for all the features, using Bowtie2 (Langmead and Salzberg, 2012).
Differential accumulation was done using DESeq2 (Love et al., 2014) and all plots were generated using ggplot2 (Wickham, 2016) packages in R environment.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Count files
 
Submission date Mar 22, 2021
Last update date Apr 01, 2022
Contact name Patricia Baldrich Gonzalez
E-mail(s) pbaldrich@ucdavis.edu
Organization name University of California - Davis
Department Genome Center
Lab Meyers Lab
Street address 451 Health Sciences Dr., Davis, CA 95616
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL24270
Series (2)
GSE169324 The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA [ncRNA-Seq]
GSE169434 The Arabidopsis F-box protein FBW2 degrades AGO1 to avoid spurious loading of illegitimate small RNA
Relations
BioSample SAMN18419053
SRA SRX10409411

Supplementary file Size Download File type/resource
GSM5195660_10016_chopped.txt.gz 16.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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