|
| Status |
Public on Sep 01, 2017 |
| Title |
lefko1 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: lefko1
|
| Growth protocol |
Arabidopsis thaliana seeds were surface-sterilized and sown in Petri dishes containing 0.5x Murashige and Skoog (MS) medium (Duchefa) pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma). After 24 hr of stratification at 4°C, seedlings were positioned to grow vertically after germination at 22°C in a Fitotron growth chamber under a long photoperiod with 16h of light and 8h of darkness per day and 100 μmol m–2 s–1 light intensity. Seedlings transferred to pots to grow until maturity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Globular to heart stage lefko2 mutant and wild-type Arabidopsis embryos were dissected from siliques. Total RNA was extracted using the NucleoSpin Plant RNA kit (Macherey-Nagel, Düren, Germany) with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of the RNA were assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).
Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”
Differential alternative splicing events were detected for lefko1 and wild-type using rMATS.
genome build: Arabidopsis genome reference (TAIR10)
processed data files format and content: Excel file with alternative splicing enents (Intron retention, 5’ and 3’ alternative start site, exon skipping) including Gene ID and coordinates.
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Polydefkis Hatzopoulos |
| E-mail(s) |
[email protected]
|
| Phone |
+302105294321
|
| Organization name |
Agricultural University of Athens
|
| Department |
Biotechnology
|
| Lab |
Molecular Biology
|
| Street address |
Iera Odos 75
|
| City |
Athens |
| ZIP/Postal code |
11142 |
| Country |
Greece |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE94576 |
Next Generation RNA Sequencing reveals defects in nuclear and chloroplast mRNA maturation of Arabidopsis thaliana lefko2 mutant |
|
| Relations |
| BioSample |
SAMN06308511 |
| SRA |
SRX2541291 |
