|
| Status |
Public on Aug 31, 2024 |
| Title |
control_6_root_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Roots
ecotype: Col-0
treatment: mock
time point: 6 hours
|
| Treatment protocol |
Liquid J-P media supplemented with 30 µM As(V) for the indicated times
|
| Growth protocol |
Plants were grown on horizontal plates with Johnson’s medium (1 mM Pi) for 7 days and transferred to J-P plates for 2 days. Then, they were treated with liquid J-P supplemented with 30 µM As(V) for the indicated times. Each sample consisted on 60 seedlings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using High Pure RNA Isolation kit (Roche)
Stranded mRNA-seq libraries were generated using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions.
Libraries were sequenced at single-end 50 bp in the Illumina Hi-Seq 2500 System at the Salk In stitute’s Next Generation Sequencing Core Facility
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Raw reads were aligned to the Arabidopsis Information resource (TAIR10) genome using STAR (v2.5.4) with default parameters
Mapped reads were counted by HTSeq (v0.6.0)
Normalization and differential expression analysis with EdgeR
Assembly: TAIR10
Supplementary files format and content: Text format with two columns: geneID and FPKM per gene
|
| |
|
| Submission date |
Feb 05, 2024 |
| Last update date |
Aug 31, 2024 |
| Contact name |
Jose M. Franco-Zorrilla |
| Organization name |
Centro Nacinal de Biotecnologia-CSIC
|
| Department |
Plant Molecular Genetics
|
| Street address |
Darwin, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE255065 |
GLABRA2 Transcription Factor integrates Arsenic tolerance with cell differentiation in Epidermal Cells [Exp1] |
| GSE255067 |
GLABRA2 Transcription Factor integrates Arsenic tolerance with cell differentiation in Epidermal Cells |
|
| Relations |
| BioSample |
SAMN39831271 |
| SRA |
SRX23534712 |
