|
| Status |
Public on May 05, 2022 |
| Title |
veg2.3 |
| Sample type |
SRA |
| |
|
| Source name |
veg2-1_inflorescenceapex
|
| Organism |
Pisum sativum |
| Characteristics |
ecotype: NGB5839
genotype/variation: veg2-1
tissue: inflorescence apex
|
| Growth protocol |
Plants were grown in a greenhouse at 21 ºC day 16 ºC night and under long-day (LD) photoperiod (16h light / 8h darkness). When needed to maintain LD photoperiod conditions natural light was supplemented with supplementary lighting (400W Phillips HDK/400 HPI (R)(N)). Plants were irrigated periodically using Hoagland Nº1 solution supplemented with oligoelements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq experiments, inflorescence apex samples (three biological replicates) from pea wild type, NGB5839 line, and veg1, pim and veg2 mutants plants were collected at floral transition, when the primary stem plant had formed 10 nodes (approximately 4 weeks after germination). Each biological replicate consisted of 3-4 inflorescence apices. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Turbo DNA-free kit INVITROGEN; Ref-AM1907) following the manufacturer’s instructions. The quality of the RNA was checked on an Agilent 2100 Bioanalyzer instrument using the RNA6000 nano kit.
Strand-specific RNA libraries were constructed using the TruSeq stranded mRNA kit (Illumina). Libraries were sequenced in a Illumina HiSeq 2500 to produce 50-nucleotide single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For RNA-seq analyses, ribosomal RNA sequences were filtered out using SortMeRNA (Kopylova et al., 2012)
Sequences of adapters were trimmed from the remaining reads using Trimmomatic (Bolger et al., 2014)
The trimmed sequences were then aligned against the Pea transcriptome using STAR (Dobin et al., 2013) and reads were counted with HTSeqCount (Anders et al., 2015)
DESeq2 with default parameters was used to perform differential expression analysis (Love et al., 2014)
Identification of genes with opposite expression patterns was performed by constructing Venn Diagrams with the online tool Venny (Oliveros, 2007-2015). Genes with opposite expression pattern in veg1 and pim samples were visualized in a heatmap created with the tool ClustVis (Metsalu et al., 2015).
Genome_build: PsUniLowCopy database, Ps Cameor database
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 05, 2021 |
| Last update date |
May 05, 2022 |
| Contact name |
Marcos Serra |
| E-mail(s) |
msp.marcosserra@gmail.com
|
| Organization name |
Instituto de Biología Molecular y Celular de Plantas Primo Yúfera (IBMCP) CSIC
|
| Street address |
Carrer de l'Enginyer Fausto Elio
|
| City |
Valencia |
| State/province |
Comunidad Valenciana |
| ZIP/Postal code |
46022 |
| Country |
Spain |
| |
|
| Platform ID |
GPL25225 |
| Series (1) |
| GSE188301 |
Identification and characterization of putative targets of VEGETATIVE1/FULc, a key regulator of development of the compound inflorescence in pea and related legumes |
|
| Relations |
| BioSample |
SAMN22933897 |
| SRA |
SRX13014155 |
