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Sample GSM3476309 Query DataSets for GSM3476309
Status Public on Nov 17, 2018
Title A1: WT_PAC_rep1
Sample type SRA
Source name Seven-day-old seedlings
Organism Arabidopsis thaliana
Characteristics accession: Nossen
tissue: whole seedlings
genotype/variation: wild-type (No-0)
treatment: 10 μM PAC
Extracted molecule total RNA
Extraction protocol Total RNAwas extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instructions, treated with the DNase Kit (Ambion), and then frozen at −80°C until analyzed.RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Truseq Stranded mRNA Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Illumina Casava1.8 software used for basecalling.
Raw data preprocessing (clipping adapters, and filter sequences <20 nt, 3’ end quality-trimmed threshold Q28) :cutadapt v1.8.3. FASTQC (v0.11.5) was used to assess data quality
All sequenced libraries were mapped to the Arabidopsis thaliana genome (Arabidopsis_thaliana.TAIR10.22) with GTF information (Arabidopsis_thaliana.TAIR10.22.gtf) using TopHat(v.2.1). Seqmonk v.1.35 was used to generate per gene raw count matrix from unique mapped reads with the same GTF file used for the alignment step (opposing strand specific, merge transcript isoforms).
Differential expression analysis performed with DESeq2 v.1.16.1 and edgeR v.3.0.2 (P-adj.value cutoff 0.05)
Genome_build: Arabidopsis_thaliana.TAIR10.22
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.
Submission date Nov 16, 2018
Last update date Nov 17, 2018
Contact name David Alabadi
Phone 34963877723
Organization name Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)
Department Biologia del Desarrollo
Lab 2.08
Street address Av de los Naranjos s/n, Campus UPV, Edificio 8E
City Valencia
State/province Valencia
ZIP/Postal code 46022
Country Spain
Platform ID GPL19580
Series (1)
GSE122617 Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction
BioSample SAMN10435151
SRA SRX5017288

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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