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Sample GSM2385864 Query DataSets for GSM2385864
Status Public on Jan 01, 2018
Title PEP1_R1_apex
Sample type SRA
Source name apices
Organism Arabis alpina
Characteristics cultivar: Pajares
age: 2 weeks-old under long-day photoperiod
genotype/variation: pep1-1 mutant
tissue: apices
Treatment protocol Apices or leaves from wild type or pep1-1 mutant were collected after two weeks at ZT8.
Growth protocol Seeds were sown on soil and grown at 22°C for 2 weeks in a long day photoperiod
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted with Rneasy Plant Moni Kit (Qiagen) following manufacture´s protocol. To estimate the quality of the RNA, samples were measured with the Agilent 2100 Bioanalyzer using Agilent RNA high sensitivity CHIP
Libraries were prepared following the TruSeq RNA Sample preparation guideline (Illumina)
4µg of total RNA were polyA-purified, fragmented and first-strand cDNA synthesized by reverse transcriptase (SuperScript II-Invitrogen) and random hexamers. This was followed by RNA degradation and second strand cDNA synthesis. End repair process and adittion of a single ‘A’ nucleotide to the 3’ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included quality control and quantification. All libraries were pooled before sequencing
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Low-quality reads in the raw data (FASTQ files) were filtered out and reads kept were then mapped to the Arabis alpina reference assembly V3 (Willing et al, 2015) using TopHat with the GTF file used in (6) (--min-anchor-length 10; --max-multihits 5; library-type fr-unstranded)
Count tables for raw counts were obtained from bam files using coverageBed.
Differential gene expression was estimated using DESeq2 package 1.10.0 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
Genome_build: Arabis alpina (version from Willing et al 2015, Nature Plants, 1), see (Version 3)
Supplementary_files_format_and_content: raw counts
Submission date Nov 08, 2016
Last update date May 15, 2019
Contact name Julieta L Mateos
Organization name Fundacion Instituto Leloir
Street address Av. Patricias Argentinas 435
City Buenos Aires
ZIP/Postal code C1405BWE
Country Argentina
Platform ID GPL22647
Series (1)
GSE89638 Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
BioSample SAMN05991957
SRA SRX2335980

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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