|
| Status |
Public on Mar 01, 2021 |
| Title |
vim1-3_23C_B |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: vim1-3
developmental stage: boyes: 1.0
tissue: seedlings
treatment: 23°C
|
| Treatment protocol |
Seedlings were grown either at 23°C or 29°C according to the sample
|
| Growth protocol |
Seeds were surface-sterilized by treatments with 70% EtOH and 5% hypochloryte-1% SDS, washed and stratified at 4°C for 2 days to obtain homogeneous germination. Seedlings were grown at 23°C or 29°C on solid half-strength Murashige and Skoog (MS/2) medium (Duchefa), under long day conditions (16h light, 95μE.m-2.sec-1/8h dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Robosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b)
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sampla
|
| |
|
| Submission date |
Feb 28, 2021 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Thomas Blein |
| E-mail(s) |
thomas.blein@cnrs.fr
|
| Organization name |
CNRS
|
| Lab |
IPS2
|
| Street address |
Avenue des Sciences
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE167879 |
The lncRNA APOLO and the methylcytosine-binding protein VIM1 are thermomorphogenesis regulators |
|
| Relations |
| BioSample |
SAMN18089702 |
| SRA |
SRX10188855 |
