Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 24
Release date: Mar 1 2015
Last update date: Mar 1 2015
Access: Public
Dataset link Comparative transcriptome profiles of cotton (G. hirsutum L. cv. Bikaneri narma) during boll development stages under bollworm infested biotic stress

Experimental Protocol


Cotton plants (G. hirsutum L. cv. Bikaneri narma) were grown under field condition. Helicoverpa armigera (cotton bollworm) second instar larvae was released at the time of flower opening and covered with polythene bag to prevent insect escape and tagged. The infested flowers were collected after 8 hrs infestations and labeled as 0 dpa. Likewise after two and five day’s infestation the bolls were collected and labelled as 2 and 5 dpa, respectively. After five days the insect was removed from bolls and left the bolls for up to 10 days and collected then labeled as 10 dpa. Meanwhile respective control samples also tagged and collected. Total RNA was isolated from control (WT) and biotic stress (bollworm infested) induced samples collected at 0, 2, 5 and 10 dpa boll development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturer’s protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2 transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

Repositories


GEO

GSE55511

ArrayExpress

E-GEOD-55511

BioProject

PRJNA239815

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Contact


Mogilicherla Kanakachari