|
| Status |
Public on Jun 05, 2024 |
| Title |
Pruned.3 |
| Sample type |
SRA |
| |
|
| Source name |
Shoot Apical Meristem
|
| Organism |
Pisum sativum |
| Characteristics |
tissue: Shoot Apical Meristem
genotype: Cameor Wild Type
developmental stage: Continiously deflowered, SAM Active
|
| Treatment protocol |
Samples were collected at different stages of development: 1.- Proliferative: SAM was collected of young plants that just started flowering. The samples were collected after the production of the first flower bud, before anthesis. 2.- GPA (UPDATED TO PA): SAM was collected just when plants undergo Proliferative Arrest. 3.- Pruned: SAM collected the same day as 2, but in plants that had been continiously pruned (never sensed seeds), avoiding the arrest of the meristem. 4.- Reactivated: SAM collected 24 hours after removing all fruits and flowers of arrested plants. 4 biological replicates for each sample. Shoot apical meristems were collected macroscopically, by removing as much leaves and flower buds as possible.
|
| Growth protocol |
Pisum sativum plants were grown in standard conditions in vermiculite (hydroponic growth with automatic watering). Plants were watered with Hoagland No.1 solution suplemented with trace elements. Greenhouse conditions: Long Day photoperiod (16 hours of light and 8 hours of darkness) with natural light supplemented with artificial light using 400 W mercury vapor lamps. Temperature fluctuated between 21.5ºC during the day and 15ºC during the night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from Shoot Apical Meristem samples at the different stages described 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.
Eukaryotic Transcriptome Library/Strand specific libray (mRNA-seq poly A enrichment) was constructed using Illumina NovaSeq 6000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were cleaned from adaptors and low-quality regions using cutadapt.
Clean reads were mapped to Pisum sativum genome using HISAT2.
Per gene read counting was done using htseq-count.
DESeq2 with default parameters was used to perform differential expression analysis.
Assembly: Pisum sativum v1a
Supplementary files format and content: TSV (tab-separated values) text file with per gene read counts for each sample.
|
| |
|
| Submission date |
Nov 06, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Javier Forment |
| E-mail(s) |
jforment@ibmcp.upv.es
|
| Organization name |
Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)
|
| Street address |
Ingeniero Fausto Elio, s/n
|
| City |
Valencia |
| ZIP/Postal code |
46022 |
| Country |
Spain |
| |
|
| Platform ID |
GPL32857 |
| Series (1) |
| GSE247124 |
Identification of factors that modulate Proliferative Arrest under the influence of seeds |
|
| Relations |
| BioSample |
SAMN38122687 |
| SRA |
SRX22385091 |
