|
| Status |
Public on Sep 17, 2021 |
| Title |
4BI |
| Sample type |
SRA |
| |
|
| Source name |
Tubers
|
| Organism |
Solanum tuberosum |
| Characteristics |
population: Diploid hybrid 17-5
developmental stage: Fully-developed tubers
trait: Dark chip color
treatment: cold storage
|
| Treatment protocol |
After harvest, tubers were ground in liquid nitrogen and freezed in -80°C untill use.
|
| Growth protocol |
Potato tubers were planted in plastic pots filled with soil. Plants grew under tent from May to October.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIZol method as described Chomczyński and Sacchi (1987).
The mRNA was isolated using Dynabeads®mRNA Purification Kit for mRNA enrichment (Ambion, 61006), and cDNA libraries were prepared using using MGIEasy RNA Directional Library Prep Set (MGI, 1000006386). The established cDNA libraries were sequenced on the BGISEQ-500 sequencing platform (BGI Genomics, China) to generate 100-bp paired-end reads (PE100).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
17-5B1
17_5A-vs-17_5B_downregulated_genes.xlsx
17_5A-vs-17_5B_upregulated_genes.xlsx
|
| Data processing |
Zebracall process Version 0.5.0.13875 used for basecalling.
The index of the reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000226075.1) was built using Bowtie v2.1.0.
Poor quality and to short reads (<30 nt) were removed from analysis.
Paired-end clean reads obtained for populations 17-5 and 17-6 were aligned to the reference genome using TopHat v2.0.9
Genome_build: GCF_000226075.1
Supplementary_files_format_and_content: xlsx files were generated using DESeq2 package
Supplementary_files_format_and_content: xlsx files, abundance measurements
|
| |
|
| Submission date |
Sep 15, 2021 |
| Last update date |
Sep 17, 2021 |
| Contact name |
Dorota Sołtys-Kalina |
| E-mail(s) |
d.soltys@ihar.edu.pl
|
| Organization name |
IHAR-PIB
|
| Department |
Mlochow Research Centre
|
| Street address |
Platanowa 19
|
| City |
Mlochow |
| ZIP/Postal code |
05-831 |
| Country |
Poland |
| |
|
| Platform ID |
GPL28958 |
| Series (1) |
| GSE184141 |
Tuber-omics in potato with the T and D types of cytoplasm showed differentially expressed genes and proteins in response to cold storage |
|
| Relations |
| BioSample |
SAMN21438489 |
| SRA |
SRX12192817 |
