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Sample GSM5106027 Query DataSets for GSM5106027
Status Public on Aug 08, 2021
Title 35S.EVD.rdr6 sRNA-seq
Sample type SRA
 
Source name inflorescence
Organism Arabidopsis thaliana
Characteristics tissue: inflorescence
overexpression: EVD
rna isolation: TRIzol
library preparation: Lexogen small RNA kit
Extracted molecule total RNA
Extraction protocol RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description sRNA
normalized_counts_sRNA.csv
Data processing Illumina Casava1.8 software used for basecalling.
Trimming of reads with bbduk v. 37.66.
Mapping to the Arabidopsis thaliana genome (TAIR10) with STAR v. 020201.
Read counting with Rsubread 1.26.1.
Read normalization with DEseq2.
P-site occupancies estimation of RIBO-seq data using RiboProfiling.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized_counts_sRNA.csv: Comma-separated text file of log2 normalized read counts.
Supplementary_files_format_and_content: RiboSeq_transcript_counts.csv: Comma-separated text file of P-site counts per codon position along all coding sequences.
 
Submission date Feb 24, 2021
Last update date Aug 08, 2021
Contact name Stefan Oberlin
E-mail(s) stefan.oberlin@ucsf.edu
Organization name ETH Zürich
Department Department of Biology
Street address Universitätstrasse 2
City Zürich
ZIP/Postal code 8092
Country Switzerland
 
Platform ID GPL17639
Series (1)
GSE167484 Innate, translation-dependent silencing of an invasive transposon in Arabidopsis
Relations
BioSample SAMN18053591
SRA SRX10166364

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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