|
| Status |
Public on Aug 09, 2021 |
| Title |
Shade_20C_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: exposed during the photoperiod of day 4 (10 h) to shade at 20C.
genotype: wild-type Columbia 0
life stage: Three day old seedlings
|
| Treatment protocol |
Three day old seedlings of the wild type Columbia were exposed during the photoperiod of day 4 (10 h) to white light at 20C, white light at 28C, shade at 20C or shade at 28C. Samples were collected at the end of the day 4.
|
| Growth protocol |
Seeds of Arabidopsis thaliana were sown on 0.8 % agar-water in Petri dishes, stratified 5-7 d at 5 ºC in darkness and transferred to a growth room at 22°C with a photoperiod of 10 h of 100 μmolm −2 s −1 of white light (400–700 nm) provided by a mixture of fluorescent and halogen lamps (red/far-red ratio = 1.1).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
In the transcriptional profiling assay total RNA was extracted with Spectrum™ Plant Total RNA Kit (Sigma) following the manufacturer’s protocols.
Libraries were prepared following the TrueSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, first-strand cDNA synthesized by reverse transcriptase (SuperScript III; Invitrogen) using random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies). Samples were pooled to create 12 multiplexed DNA libraries, which were pair-end sequenced with an Illumina HiSeq1500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Total RNA was extracted from whole seedlings
gene_counts_voom.txt
|
| Data processing |
Base-calling by default setting of Illumina HiSeq 1500
Aligment to to Arabidopsis thaliana TAIR10 genome using TopHat v2.1.1
Generation of BAM files with SAMtools V1.3
Data analysis with Voom function using R 4.0.2
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: All processed data files are .txt count tables containing the number of raw counts in each sample for all the sequenced gene trasncripts of Arabidopsis thaliana genome.
|
| |
|
| Submission date |
Nov 27, 2020 |
| Last update date |
Aug 09, 2021 |
| Contact name |
Carlos Esteban Hernando |
| E-mail(s) |
[email protected]
|
| Organization name |
Fundacion Instituto Leloir
|
| Lab |
Comparative Genomics of Plant Development
|
| Street address |
Av. Patricias Argentinas 435
|
| City |
CABA |
| State/province |
Buenos Aires |
| ZIP/Postal code |
C1405BWE |
| Country |
Argentina |
| |
|
| Platform ID |
GPL19080 |
| Series (1) |
| GSE162240 |
Functional convergence of growth responses to shade and warmth in Arabidopsis |
|
| Relations |
| BioSample |
SAMN16935546 |
| SRA |
SRX9596895 |
