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| Status |
Public on Apr 02, 2023 |
| Title |
Leaf_elf18_1 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0 (35S:5-LSTBF1-LUC)
tissue: Leaf
treatment: 1µM elf18
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| 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.
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| Growth protocol |
Plants were grown in 12h:12h light:dark cycle on soil for 4 weeks at 22C
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| 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.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Apr 02, 2021 |
| Last update date |
Apr 02, 2023 |
| Contact name |
Paul Zwack |
| E-mail(s) |
paul.zwack@duke.edu
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| Organization name |
Duke University
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| Street address |
Campus Box 90338
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE171411 |
tRNA-seq of Arabidopsis leaves during pattern-triggered immunity |
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| Relations |
| BioSample |
SAMN18605326 |
| SRA |
SRX10505870 |
| 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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