Computational protocol: GhLTPG1, a cotton GPI-anchored lipid transfer protein, regulates the transport of phosphatidylinositol monophosphates and cotton fiber elongation

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Protocol publication

[…] Based on the results of the RNA-seq analysis, a putative LTPG gene was found being up-regulated during early stages of fiber elongation. The relevant LTPG gene was amplified by PCR using cDNAs synthesized from mRNA isolated from elongating fibers of Coker312 as the template. The amplified products were cloned into the pMD19-T vector (TaKaRa, Japan) and confirmed by DNA sequencing. Expression pattern of GhLTPG1 was analyzed by Real-time quantitative PCR (qRT-PCR) and primers are listed in .qRT-PCR analysis was performed in a DNA Engine Option 3 System (MJ Research, USA) using SYBR Premix Ex-Taq (Takara, Japan). Each sample was repeated at least three times. Transcriptional changes were calculated based on the comparative ΔCT method.The deduced amino acid sequence of cotton GhLTPG1 was aligned with the Arabidopsis LTPGs using BioEdit and ClustalX. Predicted molecular weight, iso-electric point, functional domains, and amino acid signal peptides were calculated using the ExPASy online servers (http://cn.expasy.org/tools). […]

Pipeline specifications

Software tools BioEdit, Clustal W
Databases ExPASy
Application RNA-seq analysis
Organisms Gossypium hirsutum, Arabidopsis thaliana