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Status |
Public on Jun 14, 2020 |
Title |
I_PZ rep2 |
Sample type |
SRA |
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Source name |
lateral stem
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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: 4 weeks
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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).
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
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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.
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Submission date |
Jun 13, 2020 |
Last update date |
Jun 15, 2020 |
Contact name |
Anna Sergeeva |
E-mail(s) |
Anna.Sergeeva@hhu.de
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Organization name |
Heinrich Heine University
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Department |
Institute of Botany
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Lab |
Prof. Dr. Petra Bauer
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Street address |
Universitaetsstrasse 1
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City |
Dusseldorf |
ZIP/Postal code |
40225 |
Country |
Germany |
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Platform ID |
GPL26216 |
Series (1) |
GSE152417 |
Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina |
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Relations |
BioSample |
SAMN15230304 |
SRA |
SRX8541040 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4615004_02_kallisto_amb.tsv.gz |
390.7 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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