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Sample GSM5225006 Query DataSets for GSM5225006
Status Public on Apr 02, 2023
Title Leaf_Mock_1
Sample type SRA
 
Source name Leaf
Organism Arabidopsis thaliana
Characteristics genotype: Col-0 (35S:5-LSTBF1-LUC)
tissue: Leaf
treatment: mock (water)
Treatment protocol The 4th and 5th leaves of 3 plants/rep were pressure-infiltrated with either water of 1µM elf18 in water then held for 1 hour before sample collection and freezing.
Growth protocol Plants were grown in 12h:12h light:dark cycle on soil for 4 weeks at 22C
Extracted molecule total RNA
Extraction protocol Tissue was ground in liquid nitrogen and small RNA was isolated using the Zymo Direct-zol kit
RNA was incubated in 0.1M Tris pH 9.0 for 45 min at 37°C for deacylation. Demethylation was perfomed as described (Zheng et al., 2015): RNA was incubated at room temperature for 2 hours with 160 pmol of wt AlkB and 200 pmol of D135S AlkB in abuffer containing 300 nM KCl, 2mM MgCl2, 50mM (NH4)2Fe(SO4)2×6H2O, 300mM 2-ketoglutarate, 2mM L-ascorbic acid, 50mg/mL nuclease free BSA, and 50 mM MES pH 5.0. RNA was then separated on a 10% TBE-Urea gel (Novex), the region of each lane corresponding to 55 – 100 nt was isolated and RNA was recovered by passive elution into 300mM sodium acetate pH 5.2 followed by ethanol precipitation. Libraries for Illumina® sequencing were prepared using the NEBNextÒ Multiplex Small RNA Library Prep Set for Illumina® (Set1) according to the manufacturer’s instructions.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing read trimming with Trimmomatic
mapping, counting, normalization and differential expression using ARM-seq pipeline (Cozen et al., 2015 Nat. Methods)
Genome_build: Tair-10
Supplementary_files_format_and_content: tab-delimited files of normalized counts and differential expression
 
Submission date Apr 02, 2021
Last update date Apr 02, 2023
Contact name Paul Zwack
E-mail(s) paul.zwack@duke.edu
Organization name Duke University
Street address Campus Box 90338
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL19580
Series (1)
GSE171411 tRNA-seq of Arabidopsis leaves during pattern-triggered immunity
Relations
BioSample SAMN18605329
SRA SRX10505867

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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