|
| Status |
Public on May 10, 2017 |
| Title |
16C-25C 5 days C |
| Sample type |
SRA |
| |
|
| Source name |
16C-25C 5 days
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
time point: Day 5 after temperature change
temperature: 25 °C
tissue: SAM and early stages leaves
|
| Treatment protocol |
Temperature treatment: plants were moved to 25°C.
|
| Growth protocol |
Plants were grown in short day conditions (8h light/16h dark) at 16°C for 5 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample, tissue from ~10 plants was collected. Using jeweler’s forceps, leaves were removed to obtain SAM enriched tissue. Total RNA was extract using the InviTrap Spin Plant RNA Mini Kit ( REF: 1064100300) from Invitek according to the manufacturer’s protocol. DNAse treatment was performed to remove genomic DNA. DNase I digestion was performed on total RNA using Turbo DNase I from Ambion. RNA integrity was checked on 1% (w/v) agarose gel after DNase I treatment.
Samples were prepared for sequencing using the TruSeq Stranded mRNA Sample Prep kit (REF 15032613) from Illumina according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the TAIR10 genome using TopHat
Reference based full length transcript isoform reconstruction was performed using Cufflinks
MISO package was used to estimate to quantify AS-events (PSI values)
Genome_build: TAIR10
Supplementary_files_format_and_content: excel file contains PSI values 16°C and 25°C day 1, day 3 and day 5 for differential splicing events.
|
| |
|
| Submission date |
Aug 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alice Pajoro |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708lt |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE85281 |
Temperature induced changes in the Arabidopsis transcriptome |
| GSE85282 |
H3K36me3 histone modification and regulation of ambient temperature-induced alternative splicing in Arabidopsis |
|
| Relations |
| BioSample |
SAMN05520846 |
| SRA |
SRX2007116 |
