|
| Status |
Public on Jun 21, 2020 |
| Title |
181RS14 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0
cultivar: Col-0
tissue: seedling
photoperiod: Short day (8L/16D)
temperature: 22C
replicate: single
fragmentation method: NA
chip antibody: NA
|
| Growth protocol |
Arabidopsis seeds were sterilized and sown on standard half-strength Murashige and Skoog-agar (MS-agar) plates at pH 5.7. Sterilized seeds were stratified for 3 days at 4 ºC in the dark and allowed to germinate for 24 hours at 22 ºC under cool-white fluorescent light at 170 μmol m-2 s-1. The plates were then transferred to short photoperiod conditions (SDs, 8-h light and 16-h dark) at different temperatures. Seedlings were grown on plates for 10 days and harvested at the indicated time points.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
70 mg of seedlings were pooled per tube and total RNA was extracted using MagMAX™-96 Total RNA Isolation Kit (ThermoFisher) according to the manufacturer‘s instruction.
Libraries were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep FWD Kit (Illumina) according to manufacturer‘s instruction. The libraries were sequenced on the Illumina NextSeq 500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Genome_build: TAIR10
Raw fastq were uploaded to Bluebee Genomics Platform and analysed with Quantseq FWD analysis pipeline (https://www.lexogen.com/quantseq-data-analysis/). Briefly, the raw reads were trimmed with BBDuk and aligned to GTF-annotated genome with STAR.
Supplementary_files_format_and_content: *.txt: TSV table containing abundance of transcripts by STAR.
Supplementary_files_format_and_content: *.bam: Genomic alignment by STAR.
|
| |
|
| Submission date |
Sep 11, 2019 |
| Last update date |
Jun 21, 2020 |
| Contact name |
Philip Wigge |
| E-mail(s) |
wigge@igzev.de
|
| Organization name |
Cambridge University
|
| Department |
Sainsbury Laboratory
|
| Street address |
47 Bateman street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1LR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE137264 |
RNA-Seq and ChIP-Seq profiling of ELF3, an prion-like domain-containig in ELF3 that functions as a thermosensor in Arabidopsis. |
|
| Relations |
| BioSample |
SAMN12727714 |
| SRA |
SRX6830789 |
