|
| Status |
Public on Aug 09, 2022 |
| Title |
sRNA_ndx1-4_rep1 |
| 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 |
| E-mail(s) |
miskeim@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN27963128 |
| SRA |
SRX15045419 |
