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Sample GSM6965104 Query DataSets for GSM6965104
Status Public on Jun 07, 2023
Title sRNA, Col-0, rep3
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_r3_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 SAMN32886660
SRA SRX19147841

Supplementary file Size Download File type/resource
GSM6965104_srna_19-25nt_dup_col0_flower_r3.bw 8.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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