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Transcriptome sequencing of thalidomide treated limb bud of chick embryo

ABSTRACT: Purpose: The aim of this study was to compare the differentially expressed genes under thalidomide treatment in limb buds. Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 81 database. Alignment was performed using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.

ORGANISM(S): Gallus gallus

PROVIDER: GSE80309 | GEO | 2021/12/01

REPOSITORIES: GEO

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Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome

Project description:Purpose: The aim of this study is to analyse and compare the differentially expressed genes between nitric oxide treated and thalidomide treated chick embryos Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. After alignment, Cuffdiff (v2.2.0) program was used for performing differential expression analysis. Pathway analysis of differentially expressed genes was performed using DAVID program. Heat maps were constructed using R package software 3.1.0.

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Project description:Purpose: The goals of the study are to understand phenotypically different characteristics of two single clones, HN9-R and HN9-S isolated from primary Head and Neck Carcinoma HN9 and to compare transcriptome profiling to genome-wide analytic approach performed by next-generation sequencing (NGS) analysis. Methods: mRNA profiles of two single clones, HN9-R and HN9-S, were generated by sequencing using Illumina NextSeq 500 software. Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1). Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes. Results: We find total 337 DEGs (differentially expressed genes) between HN9-R and HN9-S (FPKM value of > 1, log2. Fold-change > 2, and Padj < 0.05) and that there were 178 and 159 genes of significantly increased or reduced transcripts, respectively. The level of gene expression was validated by quantitative real-time PCR using SYBR Green assay and western blotting analysis. Conclusion: The results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cells. This study provides a framework for the dissection of biological functions towards characterization of two sub-clones co-existed within a primary cancer cells.

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Identification of thalidomide modulation related genes in mesenchymal stem cells

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Prediction of Peripheral neuropathy in multiple myeloma patients receiving Bortezomib and Thalidomide: A Genetic Study based on Single Nucleotide Polymorphism Array

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