|
Status |
Public on Jun 05, 2024 |
Title |
GPA.2 |
Sample type |
SRA |
|
|
Source name |
Shoot Apical Meristem
|
Organism |
Pisum sativum |
Characteristics |
tissue: Shoot Apical Meristem genotype: Cameor Wild Type developmental stage: SAM arrested
|
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
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|
|
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.
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|
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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 (UPV-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 |
SAMN38122692 |
SRA |
SRX22385086 |