|
| Status |
Public on Mar 04, 2020 |
| Title |
OPDA1_kleb |
| Sample type |
SRA |
| |
|
| Source name |
algal suspension
|
| Organism |
Klebsormidium nitens |
| Characteristics |
treatment: OPDA
time point: 2 hours
|
| Treatment protocol |
Algal discs were transferred to a 12-well plate containing 2 ml liquid 0.5 Gamborg’s B5 mock or OPDA 25 µM, incubated for 2 hours on a shaker (120 rpm) and then the algae were frozen in liquid nitrogen and ground to a fine powder.
|
| Growth protocol |
Droplets of algal suspension from a fully-grown plate were plated on fresh 0.5 Gamborg’s B5 plates and incubated for one month
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Favorgen plant RNA extraction kit including DNAse treatment
The RNA-seq library was prepared by the Beijing Genomics Institute, using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with HISAT2
Summarization of reads was performed with HTSeq-count program
Normalization and differential expression analysis with DESeq2
Genome_build: klebsormidium_Scaffolds_v1.0
http://www.plantmorphogenesis.bio.titech.ac.jp/~algae_genome_project/klebsormidium/
Supplementary_files_format_and_content: Text format with two columns: gene_ID and raw reads per gene
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
Mar 06, 2020 |
| Contact name |
Jose M. Franco-Zorrilla |
| Organization name |
Centro Nacinal de Biotecnologia-CSIC
|
| Department |
Plant Molecular Genetics
|
| Street address |
Darwin, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL27861 |
| Series (2) |
| GSE141417 |
An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance [seq] |
| GSE141430 |
An Ancient COI1-independent Function for Reactive Electrophilic Oxylipins in Thermotolerance |
|
| Relations |
| BioSample |
SAMN13476521 |
| SRA |
SRX7264501 |
