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Sample GSM4615007 Query DataSets for GSM4615007
Status Public on Jun 14, 2020
Title II_PZ rep1
Sample type SRA
 
Source name lateral stem
Organism Arabis alpina
Characteristics genotype: perpetual flowering 1-1 (pep1-1)
tissue: whole 1st internode from the PZ of the lateral stem from 1st and 2nd node of the main axis
age: 5 weeks
Growth protocol Plants were grown on potting soil (Vermehrungssubstrat, Stender GmbH, Schermbeck, Germany) with a humidity of 70 % in a plant growth chamber (Percival Scientific, CLF Plant Climatics) under controlled long-day conditions (16 h light and 8 h dark, at 20 °C).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer‘s instructions, including DNase I digestion via the RNase-Free DNase Set to remove traces of genomic DNA (Qiagen, Hilden, Germany).
Libraries were constructed with the Illumina TruSeq® Stranded mRNA Library Prep kit (Illumina Technologies). Double-stranded cDNA was purified for end repair, adaptor ligation, and DNA fragment enrichment.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls were performed and demultiplexed using bcl2fastq2.
Sequenced reads were trimmed for adapter sequence and masked for low-complexity or low-quality sequence, then mapped to theArabis_alpina.MPIPZ.V5 reference transcriptome using kallisto.
TSV files with TPM (transcripts per million) values were generated using kallisto.
Average insert length information was extracted from the command line output of kallisto.
Genome_build: Arabis_alpina.MPIPZ.V5
Supplementary_files_format_and_content: TSV files were generated using kallisto. Besides normalized TPM values they contain counts and length information.
 
Submission date Jun 13, 2020
Last update date Jun 15, 2020
Contact name Anna Sergeeva
E-mail(s) Anna.Sergeeva@hhu.de
Organization name Heinrich Heine University
Department Institute of Botany
Lab Prof. Dr. Petra Bauer
Street address Universitaetsstrasse 1
City Dusseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL26216
Series (1)
GSE152417 Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina
Relations
BioSample SAMN15230302
SRA SRX8541023

Supplementary file Size Download File type/resource
GSM4615007_04_kallisto_amb.tsv.gz 386.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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