|
| Status |
Public on Feb 27, 2019 |
| Title |
pep1-1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
3 weeks old plants
|
| Organism |
Arabis alpina |
| Characteristics |
tissue: dissected shoot apices
genotype: pep1-1
cultivar: Pajares
|
| Growth protocol |
Plants are grown for 3 weeks at long day 16h light : 8 h dark.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to manufacturer's instructions
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using TruSeq type RNA kit (Illumina) at the Cologne Genome Centre and sequenced as 100-bp single-end reads on HiSeq2500 (Illumina) instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Filtered for per base Phred score greater than 25
Mapping of RNA-seq reads done by TopHat with default parameters
Expression Value was estimated by Cuffdiff considering all replicates
Differential gene expression analysis performed by Cuffdiff which uses t-test and pval calculation for each comparison
Adjustment of pval was done by Cuffdiff using Benjamini-Hochberg method
Further analysis, like filtering on the basis of logFC and padj were performed by various application of Linux
Genome_build: Arabis alpina V4 genome
Supplementary_files_format_and_content: excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 01, 2018 |
| Last update date |
Feb 27, 2019 |
| Contact name |
Maria Albani |
| Organization name |
University of Cologne
|
| Department |
Botanical institute
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Köln |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23515 |
| Series (1) |
| GSE117977 |
The Arabis alpina APETALA2 orthologue delays flowering by repressing floral meristem identity genes during vernalization |
|
| Relations |
| BioSample |
SAMN09753065 |
| SRA |
SRX4496260 |
