|
| Status |
Public on Oct 27, 2021 |
| Title |
Leaf, low phytotoxic potential, B2 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Solanum tuberosum |
| Characteristics |
tissue: Leaf
population: Diploid hybrid 15-1
developmental stage: Full anthesis
phenotype: High glycoalkaloids, low phytotoxic potential
treatment: untreated
|
| Treatment protocol |
At stage of full anthesis, leaves were collected, ground in liquid nitrogen and freezed in -80°C until use.
|
| Growth protocol |
Potato plants were planted in plastic pots filled with soil. Plants grew in greenhouse 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 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 |
| |
|
| 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 bulks A and B were aligned to the reference genome using TopHat v2.0.9.
Assembly: GCF_000226075.1
Supplementary files format and content: csv files were generated using DESeq2 package.
Supplementary files format and content: all_samples_raw_count.xlsx: Excel file includes abundance measurements.
|
| |
|
| Submission date |
Oct 24, 2021 |
| Last update date |
Mar 11, 2022 |
| 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) |
| GSE186482 |
Involvement of flavonol synthase/flavanone 3-hydroxylase-like in expression of phytotoxic potential of potato (Solanum sp.) |
|
| Relations |
| BioSample |
SAMN22549365 |
| SRA |
SRX12755582 |
