|
| Status |
Public on Mar 23, 2021 |
| Title |
v7_m1 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
age: 5 days
genotype: vnd7
treatment: mock
|
| Treatment protocol |
Seedlings were transferred to plates containing 1µM ABA or mock and treated for 8h.
|
| Growth protocol |
Seeds were surface sterilized with ethanol, plated on 1/2MS+MES+bactoagar plates on mesh and stratified for 2 days. Seedlings were grown for 5 days in long day conditions, 16h light (22 C) and 8h darkness (20 C) at light intensity of 110µE/m2/s. Per sample 50-100 seedlings were pooled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNAeasy Plant Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext®UltraTM RNA Library Prep Kit for Illumina® for paired-end sequencing with read length 150
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Mapping to Arabidopsis thaliana reference genome with Hisat2
Generating of Count files with HTSeq
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 22, 2021 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Frauke Augstein |
| E-mail(s) |
[email protected]
|
| Organization name |
Uppsala University
|
| Department |
IOB
|
| Lab |
Carlsbecker
|
| Street address |
Almas Allé 5
|
| City |
Uppsala |
| ZIP/Postal code |
SE-756 51 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE169365 |
Transcriptomic changes upon ABA treatment dependent on VND transcription factors |
| GSE169367 |
Blocking ABA-signaling and ABA-treatment; ABA treatment dependence on VND transcription factors |
|
| Relations |
| BioSample |
SAMN18432322 |
| SRA |
SRX10413900 |
