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Sample GSM5267595 Query DataSets for GSM5267595
Status Public on Apr 28, 2021
Title ski2-5 R3 Exp3
Sample type SRA
Source name inflorescences
Organism Arabidopsis thaliana
Characteristics genotype: ski2-5
experiment: Experiment3
Growth protocol seeds were surface-sterilized, plated on 1xMS agar plates and 10 DAG seedlings were transferred to soil and grown in percival growth chambers with a cycle of 16 h light (21 ºC, 70% relative humidity)/ 8 h darkness (16 ºC, 70% relative humidity)
Extracted molecule total RNA
Extraction protocol inflorescences were collected and snap-frozen in liquid nitrogen. Total RNA was extracted with Trizol reagent according to the instructions from the manufacturer. After the RNA extraction, the RNA was treated for polysaccharides with an additional mild EtOH precipitation.
1 µg of total RNA was used as input per sample. The libraries were constructed with the NEBNext small RNA libraries preperation kit #E7300 following the protocal of the kit.
miRNA-Seq (or rather small RNA seq as you do not only sequence miRNAs)
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
Description small RNA
Data processing trimming with cutadapt v.2.4
mapping with STAR_2.6.0a
reads were quantified with featureCounts from subread-1.6.3 using an Araport11 GFF3 file modified to also include intergenic regions with a gene accession number as 1, 2, 3 etc.
reads were normalized and transformed with DESeq2
DESeq2 analysis was performed and the mutant vs WT results were extracted with an alpha cut-off = 0.1
Genome_build: TAIR10
Supplementary_files_format_and_content: matrix of gathered DESeq2 contrasts from each mutant genotype vs WT
Submission date Apr 27, 2021
Last update date Apr 28, 2021
Contact name Peter Brodersen
Organization name University of Copenhagen
Department Department of Biology
Lab Peter Brodersen Lab
Street address Ole Maaløes Vej 5
City København N
ZIP/Postal code 2200
Country Denmark
Platform ID GPL19580
Series (1)
GSE173426 Nuclear and cytoplasmic RNA exosomes and PELOTA limit miRNA-induced secondary siRNA production
BioSample SAMN18880074
SRA SRX10687667

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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