|
| Status |
Public on Jun 20, 2024 |
| Title |
Rep1 Zone 3 |
| Sample type |
SRA |
| |
|
| Source name |
Root_Zone 3
|
| Organism |
Picea abies |
| Characteristics |
tissue: Root
segment/zone: Zone 3
|
| Growth protocol |
The seedlings were grown on plate until approximately 2 days after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For zone samples, the total RNA samples were isolated using protocol adapted from Azevedo et al¸ 2003. After extraction with chloroform + isoamyl alcohol, the RNA was washed and eluted on-column using RNeasy kit (Qiagen). For LCM samples, the total RNA was extracted using RNAqueous - Micro Kit (Ambion).
Libraries were prepared according to standard Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sector3-A_S28_L003
processed data: Counts_Sample1234_Zones
|
| Data processing |
Sequencing was done by Scilife Lab (Uppsala, Sweden) and we received the raw data
Filtering was done using SortmeRNA and Trimmomatic
Mapping was done against the Picea abies genome v1.0 using STAR
Read counting was done using HTSeq-Count
Supplementary_files_format_and_content: Matrix table containing all raw counts of all samples
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Van Nguyen |
| Organization name |
Uppsala University
|
| Street address |
Almas Allé 5
|
| City |
Uppsala |
| ZIP/Postal code |
75651 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19695 |
| Series (1) |
| GSE178534 |
Transcriptomes of Norway spruce seedling roots |
|
| Relations |
| BioSample |
SAMN19795559 |
| SRA |
SRX11187549 |
