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Sample GSM6077019 Query DataSets for GSM6077019
Status Public on Aug 09, 2022
Title sRNA_ndx1-4_rep3
Sample type SRA
Source name 10-day-old seedling
Organism Arabidopsis thaliana
Characteristics tissue: Seedling
age: 10 days
genotype: ndx1-4
Growth protocol 2 g of 10-day-old seedlings of Col-0, and ndx1-4 plants were harvested.
Extracted molecule total RNA
Extraction protocol Total RNA was purified from Col-0 and ndx1-4 seedlings (3-3 biological replicates) using phenol-chloroform extraction. The quality of total RNA samples was checked by an Agilent bioanalyzer (RIN > 9).
Small DNA libraries were prepared according to Illumina’s NEBNext® Multiplex Small RNA Library Prep protocol. sRNA-seq libraries were sequenced using an Illumina NextSeq500 instrument with 1x50 bp reads.
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
Description A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Data processing The results were analysed using the sRNAnalyzer pipeline as follows: Illumina adapters were trimmed by Cutadapt and reads were then size selected in the 19-25 nt range.
Using sRNAnalyzer, size selected reads were aligned to the miRbase database and a recently published comprehensive small RNA locus database.
Differential sRNA expression between Col-0 and ndx1-4 samples was determined by DESeq2 and results were plotted in R.
Assembly: A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0).
Supplementary files format and content: tsv files contain the expression data (read counts) from col0 and ndx1-4 samples (3-3 replicas), log2 fold change.
Submission date Apr 28, 2022
Last update date Aug 09, 2022
Contact name Márton Miskei
Organization name University of Debrecen
Department Department of Biochemistry and Molecular Biology
Street address Nagyerdei Krt. 48.
City Debrecen
ZIP/Postal code 4032
Country Hungary
Platform ID GPL19580
Series (2)
GSE201840 Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [sRNA-seq]
GSE201841 Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis
BioSample SAMN27963126
SRA SRX15045421

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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