2025-12-13
ENA first public
ERC000011
ENA-CHECKLIST
Center of Excellence for Sustainable Food Security, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
INSDC center name
public
INSDC status
ERS27370196
SRA accession
E-MTAB-16215:Sample 7
Submitter Id
ArrayExpress
broker name
not collected
collection date
Asian cultivated rice
common name
Nipponbare
cultivar
Protocols: Total RNA was extracted from rice mesocotyls of the OsCCD4b CRSIPR mutant and the overexpression lines using TRI-Reagent with Direct-zol RNA MiniPrep Kit according to the manufacturer's instructions (Zymo Research). Seedlings that were nine days old, with 4-5 seedlings grouped together for each sample, were collected in a dark room illuminated by green lights. The quality and quantity of RNA were assessed using the NanoDrop 6000.  GO analysis has been performed. The vermiculite experiment was performed as described by Patil et al. (2019) with some modifications. Initially, 250 ml of vermiculite was added to the glass vessels (6 cm diameter, 18 cm height). Then, approximately twenty (dry) seeds were placed on this layer, and following this, 500 ml of vermiculite was added on top of the seeds. Lastly, 400 mL of Milli-Q water (pH 5.8) was added to each bottle, and each was tightly closed and incubated in complete darkness above conditions for 10 days The vermiculite experiment was performed as described by Patil et al. (2019) with some modifications. Initially, 250 ml of vermiculite was added to the glass vessels (6 cm diameter, 18 cm height). Then, approximately twenty (dry) seeds were placed on this layer, and following this, 500 ml of vermiculite was added on top of the seeds. Lastly, 400 mL of Milli-Q water (pH 5.8) was added to each bottle, and each was tightly closed and incubated in complete darkness above conditions for 10 days To identify differentially expressed genes, the DESeq. 2R package (version 1.20.0) was employed under the criteria of an adjusted p-value ≤ 0.05 and a fold change (FC) ≥ 0.58.  Total RNA was extracted from rice mesocotyls of the OsCCD4b CRSIPR mutant and the overexpression lines using TRI-Reagent with Direct-zol RNA MiniPrep Kit according to the manufacturer's instructions (Zymo Research). Seedlings that were nine days old, with 4-5 seedlings grouped together for each sample, were collected in a dark room illuminated by green lights. The quality and quantity of RNA were assessed using the NanoDrop 6000.  Illumina Novaseq platform. Library preparation, sequencing, and subsequent data analysis were conducted by Novogene Technology.
description
Os4b-OE
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Oryza sativa
organism
Oryza sativa
organism
mesocotyl
organism part
Oryza sativa
scientific_name
Sample 7
title