|
| Status |
Public on Jun 07, 2023 |
| Title |
sRNA, Col-0, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
flower
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: flower
developmental stage: 5-week-old
ecotype: Col-0
genotype: wild type
|
| Growth protocol |
Inflorescence tissues of 5-week-old Col-0 and ndx1-4 flowering plants were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from Col-0 and ndx1-4 flowers using the phenol-chloroform extraction method. 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.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
col0_r2_count
|
| Data processing |
NGS libraries were sequenced (1x50 bp reads) using an Illumina NextSeq 500 instrument.
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 (adjusted p-value < 0.05).
For data visualisation reads were aligned to the A. thaliana reference sequence (TAIR10) using bowtie2. Duplicate reads have not been filtered out. We used deepTools bamCoverage to create RPKM (Reads per Kilobase per Million) normalized coverage files.
Assembly: A. thaliana (TAIR10)
Supplementary files format and content: Coverage data (bigWig) files are RPKM normalized read coverage data of mapped reads.
Supplementary files format and content: Differentially expressed sRNA data (tab-delimited text file) is a result of DESeq2 analysis between Col-0 and ndx1-4 samples. Data table includes count, log2(Fold Change), adjusted p-value of differentially expressed sRNAs.
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Lorant Szekvolgyi |
| Organization name |
University of Debrecen
|
| Department |
Department of Pharmacy
|
| Lab |
Genome Architecture and Recombination Research Group
|
| Street address |
Egyetem ter 1.
|
| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE223590 |
Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence [ncRNA-Seq] |
| GSE223591 |
Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX) deficient Arabidopsis inflorescence |
|
| Relations |
| BioSample |
SAMN32886661 |
| SRA |
SRX19147840 |
