|
| Status |
Public on Aug 01, 2015 |
| Title |
At_H6_R1 |
| Sample type |
SRA |
| |
|
| Source name |
rosette leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: Col-0
tissue: rosettes - 5 leaves stage
exposure time: heat stress 6 h 37°C
|
| Treatment protocol |
Plants were transferred to 37°C for 6 hours (heat stress). For recovery, heat stressed plants were placed back to mock conditions for 48 hours.
|
| Growth protocol |
Plants were grown for 3 weeks on soil in a growth chamber under long day (16 h light: 8 h dark) regime at 21°C (mock treatment).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves were dissected with a razor blade, flash frozen in liquid nitrogen and total RNA was extracted using the RNeasy Mini Kit (Qiagen) with additional on column DNAse I (Roche) digest
RNA libraries were prepared using RNA TruSeq kit (Illumina) using standard protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 3
|
| Data processing |
read quality control (FastQC)
low quality read trimming (FASTX tools)
mapping to Arabidopsis TAIR10; and Alyrata_107 genome assembly (TopHat)
retrieving number of reads per gene coordinates (qualimap)
Genome_build: TAIR10 for samples 1-6; Alyrata_107 genome assembly for samples 7-12 and gene annotation v2 (Rawat et al. 2015)
Supplementary_files_format_and_content: EXCEL file, readcounts per gene for each of the libraries and RPKM values
|
| |
|
| Submission date |
May 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ales Pecinka |
| E-mail(s) |
pecinka@ueb.cas.cz
|
| Phone |
+420 585 238 709
|
| Organization name |
Institute of Experimental Botany
|
| Department |
Centre of Plant Structural and Functional Genomics
|
| Lab |
Pecinka group
|
| Street address |
Slechtitelu 31
|
| City |
Olomouc - Holice |
| ZIP/Postal code |
783 71 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE69077 |
Comparative transcriptome analysis in response to heat stress in Arabidopsis thaliana and Arabidopsis lyrata |
| GSE81496 |
Arabidopsis lyrata gene annotation using RNA-sequencing data |
|
| Relations |
| BioSample |
SAMN03702813 |
| SRA |
SRX1034174 |
