Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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.

2017-01-01 | GSE69159 | GEO

Next Generation Sequencing to study Thalidomide mechanism in Cutaneous Lupus

Project description:Thalidomide has been shown to be effective in patients with refractory cutaneous lupus erythematosus (CLE). However, its use is still limited by its potential severe side-effects. We conducted an RNA-sequencing study using CLE skin biopsies before and after thalidomide treatment to discover its mechanism of action. Methods: Total mRNA from skin biopsies from 10 CLE patient have been processed by RNA-seq in duplicate using Illumina Hiseq 2000 sequencing platform version 3. Application was stranded mRNA-Seq, paired-end and read length was 75bp. The sequence reads that passed quality filters were analyzed at the transcript isoform level using STAR program, RSEM program and DESeq2. Mapping was done with STAR (version 2.5.2a), quantification by RSEM (1.2.28) and differential analysis by DESeq. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to human genome (hs37d5). Average un-mapped was between 11,40-7,05 %, average unique was 80.48-76,62% and average alignment insert size was 170,00-155,00 in the 20 samples. Conclusions: Plausibles mechanisms of action for thalidomide in lupus cutaneous were discovered using this study; however, in vitro and in vivo experiments would be performed to demostrate them.

2021-12-07 | GSE162424 | GEO

Thalidomide Exerts Distinct Molecular Antileukemic Effects

Project description:Thalidomide Exerts Distinct Molecular Antileukemic Effects and Combined Thalidomide/Fludarabine Therapy is Clinically Effective in High-Risk Chronic Lymphocytic Leukemia Background: Thalidomide represents a promising immunomodulatory drug that targets both leukemia cells and the tumor microenvironment. Methods: We treated chronic lymphocytic leukemia (CLL) patients with a combined thalidomide/fludarabine regimen and monitored cellular and molecular changes induced by thalidomide in-vivo prior to fludarabine treatment. Thalidomide was given daily (100mg p.o./day) and fludarabine was administered on days 7-11 (25 mg/m² i.v./day) within each 4-week cycle (maximum of 6 cycles). Twenty patients received thalidomide/fludarabine as first line therapy and 20 patients were previously treated. Unmutated IgVH mutation status was found in 36 cases and 13 had high-risk cytogenetic aberrations (deletion of 17p13 or 11q22-q23). Results: The overall response rate was 80% and 25% for untreated and previously treated patients, respectively. While thalidomide effectively reduced the number of CLL cells, the number of CD3 lymphocytes showed no significant change, but the number of CD4+CD25hiFOXP3+ T-regulatory cells was significantly decreased. Gene expression profiling revealed a thalidomide induced signature containing both targets known to play a role in immunomodulatory drug action as well as novel candidate genes. Conclusions: Combined thalidomide/fludarabine therapy demonstrated efficacy in high-risk CLL patients. Furthermore, our study provides novel biological insights into thalidomide effect, which might act by enhancing apoptosis of CLL cells and reducing Tregs, thereby enabling T-cell dependent anti-tumor effect.

2009-08-21 | GSE15913 | GEO

Thalidomide induced early gene expression perturbations indicative of human embryopathy in mouse embryonic stem cells

Project description:To unravel the mechanisms of thalidomide developmental toxicity, we used microarrays to study transcriptomic changes induced by thalidomide during mouse embryonic stem cell (mESC) differentiation. C57BL/6 mESCs were allowed to differentiate spontaneously and global gene expression changes were studied using microarrays at at different time points after exposure to 0.25 mM thalidomide (THD).

2015-05-31 | GSE61306 | GEO

Brain vascular transcriptomes of mouse hyperglycemia mutants and controls

Project description:Purpose:To take a comprehensive effort in characterizing the brain vasculature gene expression upon hyperglycemia. Methods: We extracted mRNA from brain microvasculature fragments isolated from a genetic mouse model of hyperglycemia (Ins2-AKITA) and WT mice and analyzed their transcriptome with RNA sequencing The samples were sequenced on an Illumina HiSeq 2500 sequencer at the SNP&SEQ sequencing facility (Science for Life laboratory (SciLifeLab), Uppsala sequencing node). The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1) Results: Twenty-three genes were significantly regulated in mutant when compared to WT (False Discovery Rate < 0.05)

2018-12-11 | GSE113919 | GEO

LPS inflammation model and thalidomide effect using PBMC cells

Project description:In this research, we use DNA microarray analysis to clarify the gene expression responses from thalidomide in PBMC cells after lipopolysaccharide (LPS) treatment.

2011-09-30 | GSE28708 | GEO

Identification of thalidomide modulation related genes in mesenchymal stem cells

Project description:Comparison of gene expression data from thalidomide modulated- and unmodulated-MSCs from patients with idiopathic thrombocytopenic purpura (ITP).

2013-03-12 | GSE44948 | GEO

Gene expression profiling of two subclones of HN9-S and HN9-R isolated from patient-derived HN9 cancer cells

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.

2021-06-22 | GSE133201 | GEO

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

Project description:Bortezomib and thalidomide-based therapies have significantly contributed to improved survival of multiple myeloma (MM) patients. However, treatment-induced peripheral neuropathy (TiPN) is a common adverse event associated with them. Risk factors for TiPN in MM patients include advanced age, prior neuropathy, and other drugs, but there are conflicting results about the role of genetics in predicting the risk of TiPN. Thus, we carried out a genome-wide association study (GWAS) based on more than 300,000 exome single nucleotide polymorphisms (SNPs) in 172 MM patients receiving therapy involving bortezomib and thalidomide. We compared patients developing and not developing TiPN under similar treatment conditions (GEM05>65, NCT00443235). The highest-ranking SNP was rs45443101, located in the PLCG2 gene, but no significant differences were found after multiple comparison correction (adjusted p=0.1708). Prediction analyses, cytoband enrichment and pathway analyses were also performed, but none yielded any significant findings. A copy number approach was also explored, but this gave no significant results either. In summary, our study did not find a consistent genetic component associated with TiPN under bortezomib and thalidomide therapy that could be used for prediction, which makes clinical judgment essential in the practical management of MM treatment

2018-04-30 | GSE80278 | GEO

Identification of thalidomide modulation related genes in mesenchymal stem cells

Project description:Comparison of gene expression data from thalidomide modulated- and unmodulated-MSCs from patients with idiopathic thrombocytopenic purpura (ITP). This experiment consists of 3 arrays.

2013-03-12 | E-GEOD-44948 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data