|
| Status |
Public on Jan 10, 2015 |
| Title |
transcriptomic profile of atpip1;2-1 Arabidopsis thaliana mutant leaf |
| Sample type |
SRA |
| |
|
| Source name |
leaf, atpip1;2-1 mutant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia, NASC ID N519794
organ: leaf
developmental stage: 3 weeks old
genotype/variation: atpip1;2-1 mutant
|
| Growth protocol |
plants were grown on soil under standard greenhouse conditions with a 12-h photoperiod (24°C day/20°C night), 60% relative humidity, a photon flux density at plant level of about 70 to 80 µmol m-2 s-1 and at an ambient CO2 concentration of 370 µmol mol-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaf samples of 10 individual plants (3 weeks old) using RNeasy Plant Mini Kit (Qiagen, Hilden Germany) according to the manufacturer’s manual. Subsequently, 3’ UTR cDNA libraries were constructed by GATC–Biotech (Konstanz, Germany). Libraries were sequenced using the Genome Analyzer II. After quality control, raw reads were obtained from GATC–Biotech (Konstanz, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Sequencing reads were aligned to the Arabidopsis TAIR9 reference genome using BLAT (Kent, 2002). The resulting mapping file was parsed using an in-house pearl script kindly provided by A. Weber, Düsseldorf, Germany (Brautigam et al., 2008). This procedure ensured that only the mapping hit with the best match to the corresponding read was retained. Differentially expressed genes were identified by applying a Poisson statistics and a Bonferroni correction (Audic and Claverie, 1997).
Genome Build:
atpip1:2-1_counts.txt: TAIR9
atpip1:2-1.fas: TAIR9
|
| |
|
| Submission date |
Jan 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Marlies Heckwolf |
| E-mail(s) |
heckwolf@bio.tu-darmstadt.de
|
| Phone |
+496151164389
|
| Organization name |
Technische Universität Darmstadt
|
| Department |
Biology
|
| Lab |
Applied Plant Science (Prof. Kaldenhoff's Lab)
|
| Street address |
Schnittspahnstraße 10
|
| City |
Darmstadt |
| ZIP/Postal code |
64287 |
| Country |
Germany |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE34984 |
Transcriptomic changes in aquaporin PIP1;2 deficient Arabodposis plants |
|
| Relations |
| SRA |
SRX115356 |
| BioSample |
SAMN00771524 |
