|
| Status |
Public on Aug 25, 2023 |
| Title |
Col0 A |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
developmental stage: boyes: 1.0
ecotype: Col0
genotype: wild type
|
| Growth protocol |
Media = MS/2, pH 5.8, Temperature = 21°C day/ 21°c night Light = 16 hours day / 8 hours night for 12 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QuickRNA Miniprep Kit from Zymo Research and treat with DNAse according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols using Stranded mRNA Prep kit
|
| |
|
| 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. Ribosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.7.2a)
Reads were counted on each Araport11 features using featureCounts from subreads package (v1.6.5) using strand specific mode (-s 2 -O -M –fraction).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
|
| |
|
| Submission date |
Jul 01, 2022 |
| Last update date |
Aug 25, 2023 |
| 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) |
| GSE207358 |
Influence of the downregulation of the ARES lncRNA (AT4G14548) on gene regulation in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN29472820 |
| SRA |
SRX15996161 |
