 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 14, 2020 |
| Title |
IV_PZ rep2 |
| 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: 30 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 |
SAMN15230295 |
| SRA |
SRX8541030 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4615018_11_kallisto_amb.tsv.gz |
383.0 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 |
|
|
|
|
 |
