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| Status |
Public on Feb 23, 2023 |
| Title |
CO8-DA-treated pea roots, 24 h 1 |
| Sample type |
SRA |
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| Source name |
roots
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| Organism |
Pisum sativum |
| Characteristics |
cultivar: Frisson
cell type: roots
genotype: WT
treatment: CO8-DA
time: 24 h
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| Treatment protocol |
Deacetylated COs with main degree of polymerization around eight (CO8-DA): Mn = 1089, Mw = 1514, Ip = 1.39, CDS = 93% in Cl-form were used for treatment.
Four- to five-day-old seedlings of cv. Frisson were placed on the supporting foil surface in glass jars with 0.5x Jensen’s medium (control) (van Brussel et al., 1982) or 0.5x Jensen’s medium with CO8-DA (10-5 M) and incubated for 24 h. After treatment, the roots of pea seedlings were harvested for RNA extraction and gene expression analysis and immediately frozen at −80 °C.
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| Growth protocol |
Four to five-day-old pea seedlings of cultivar Frisson were used for treatment with elicitors
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| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of RNA from the roots was done using the PuroZOL RNA isolation reagent (BioRad Laboratories, California, USA). DNA was eliminated using DNAse digestion (Thermo Fisher Scientific, USA). RNA quality and quantity were determined by Nanodrop (Implen GmbH, Munich, Germany).
The RNA sequencing libraries were prepared following the guidelines for NEBNext mRNA magnetic isolation module purification kit (E7490) (https://www.neb-online.de/en/art/E7490) and NEBNext Ultra II directional RNA library prep kit for Illumina (E7760) (https://www.neb-online.de/en/art/E7770S) (New England Biolabs, USA). The quality of RNA was estimated using Bioanalyzer 2100 (Agilent Technologies, California, USA) prior to sequencing. The NEBNext Multiplex Oligos primer set for Illumina (Index Primers Set 2) (E7500S) (New England Biolabs, USA) was used for preparation. At all stages, the material was cleaned using AMPure XP beads (Beckman Coulter, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CO8_3
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| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 with default parameters
Trimmed sequence reads were mapped to Pisum_sativum_v1a (GCA_900700895.2) using bowtie2 v2.4.4 (parameters --very-sensitive)
Read count extraction and normalization were performed using RSEM v1.3.1
Assembly: Pisum_sativum_v1a (GCA_900700895.2)
Supplementary files format and content: tab-delimited text files include estimated counts for each Sample
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| Submission date |
Nov 15, 2022 |
| Last update date |
Feb 23, 2023 |
| Contact name |
Polina Kozyulina |
| E-mail(s) |
polykoz@gmail.com
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| Organization name |
ARRIAM
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| Street address |
Podbelsky chausse 3
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| City |
Pushkin |
| ZIP/Postal code |
196608 |
| Country |
Russia |
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| Platform ID |
GPL32857 |
| Series (1) |
| GSE218057 |
Transcriptomic analysis of pea plant responses to chitooligosaccharides’ treatment revealed stimulation of calcium-regulated reactions and mitogen-activated protein kinase cascade |
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| Relations |
| BioSample |
SAMN31744337 |
| SRA |
SRX18276754 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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