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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
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
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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