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Sample GSM4209381 Query DataSets for GSM4209381
Status Public on Jun 01, 2021
Title Nkd1-SRDX.24h.rep2
Sample type SRA
Source name whole seedlings
Organism Arabidopsis thaliana
Characteristics background line: Col-0
construct: Nkd1-SRDX
developmental stage: 7-day old seedling
Treatment protocol Transgene expression was induced by incubation in estradiol plates for 5h or 24h.
Growth protocol Arabidopsis seedlings grown in ½ MS plates for 7 days. Then transferred to a new ½ MS plate supplemented with Estradiol (5uM)
Extracted molecule polyA RNA
Extraction protocol RNA extractions were performed with RNAeasy Plant kit (QIAGEN) and mRNA was isolated by Poly(A) RNA Selection kit (Lexogen) from 1µg of total RNA.
RNA libraries were prepared for sequencing using Lexogen SENSE mRNA-Seq Library Prep Kit V2 following manufacturer's protocol
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing NextSeq Control Software was used to control the sequencer
RTA v2.4.11 software was used for basecalling
raw RNA-seq reads were aligned to TAIR10 genome using STAR v2.5.1 (Dubin et al doi: 10.1093/bioinformatics/bts635) (non-default parameters: --alignIntronMax 6000 --alignMatesGapMax 6000 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1). Each sample has two fastq files (sequenced on 2 lanes) that were pooled for the alignment.
RNA-seq read counts for all TAIR10 protein-coding genes were calculated using featureCounts tool from Subread (version 1.4.6) package (Liao et al, Bioinformatics, 2014)
Genome_build: TAIR10
Supplementary_files_format_and_content: process data file is a tab separated text file which contains raw read counts for Arabidopsis thaliana TAIR10 protein-coding genes in all 24 sequenced samples
Submission date Dec 06, 2019
Last update date Jun 01, 2021
Contact name Fernando Navarrete
Organization name Gregor Mendel Institute
Street address Dr. Bohr Gasse 3
City Vienna
State/province Vienna
ZIP/Postal code 1030
Country Austria
Platform ID GPL19580
Series (1)
GSE141597 Naked1 targets Topless to up-regulate Auxin signaling and suppress immunity
BioSample SAMN13499998
SRA SRX7283186

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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