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Status |
Public on Apr 01, 2022 |
Title |
hyl1fbw2_1 (AGO1-IP RNA) |
Sample type |
SRA |
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Source name |
AGO1-IP RNA
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Organism |
Arabidopsis thaliana |
Characteristics |
tissue: Seedlings ecotype: Columbia 0 replicate: 1 genotype: hyl1fbw2
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Treatment protocol |
No treatment
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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).
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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).
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
NextSeq 550 |
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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
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Submission date |
Mar 22, 2021 |
Last update date |
Apr 01, 2022 |
Contact name |
Patricia Baldrich Gonzalez |
E-mail(s) |
pbaldrich@ucdavis.edu
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Organization name |
University of California - Davis
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Department |
Genome Center
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Lab |
Meyers Lab
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Street address |
451 Health Sciences Dr., Davis, CA 95616
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City |
Davis |
State/province |
CA |
ZIP/Postal code |
95616 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN18419048 |
SRA |
SRX10409413 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5195662_10018_chopped.txt.gz |
31.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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