Dataset Information

Next-Generation Sequencing reveals the effects of MYC silencing in gastric cancer cell lines from northern Brazil

ABSTRACT: Purpose: In carcinogenesis, the stomach, the MYC gene is frequently amplified and its protein is overexpressed, which contributes to uncontrolled cell proliferation mucosal gástrica.Três cell lines were subjected to sequencing semiconductor Proton Ion before and after the silencing of MYC. These lines were originating from diffuse and intestinal histologic types and the third of a metastasis from a stomach tumor originating in a ascites. Methods: mRNA profiles were generated from three established lines of CG previously characterized by our group. AGP01 (Obtained from ascitic fluid of an intestinal-type GC), ACP02 (diffuse-type GC) and ACP03 (intestinal-type GC). The three cell lines present chromosome 8 trisomy and MYC amplification, reflecting the genetic characteristics found in gastric cancer samples from Northern Brazil. They were generated by sequencing depth in triplicate using the Sequencer ™ Ion Proton. Raw data reads Obtained by primary sequencing Were Submitted to quality control in order to calculate alignment and to assess how the reads behave When Compared to the reference human genome (Hg19 / GRCh37). The aligned reads Were mapped and quantified using TMAP. Gene expression levels Were quantified using Sailfish pack software and the RPKM (Reads Per kilobase per Million mapped reads) method was used to estimate Then expression levels gene. Results: Using analysis of an optimized workflow, we mapped more than 13 million readings sequences between our samples from the human genome. Were mapped a total of 917 up-regulated genes and 1,566 different genes down-regulated Were When comparing the expression of AGP01 non-targeting control (1C) versus AGP01 MYC-silenced (1M), with a total of 2,483 DEGS. The evaluation of ACP02 cells treated with non-targeting control (2C) versus ACP02 MYC-silenced (2M) Showed a total of 5,327 DEGS, with 1,299 up-regulated and 4,098 down-regulated genes. The total of 4,117 were found DEGS When comparing ACP03 control cells (3C) with ACP03 MYC-silenced cells, with 3,274 up-regulated and 843 down-regulated genes. Silencing of the MYC gene, allowed the detection of more than 1,000 DEGS (Differentially Expressed Genes) between the three strains that were considered significant if the False Discovery Rate (FDR) was ≤0.001, P-value <0.05, and the absolute value of the Fold change (FC) was ≥1. The analysis of DEGS showed 22% and 34% were detected with a profile down-regulated in intestinal and diffuse type, respectively. The up-regulated profile was higher in the intestinal type, with 77% of DEGS than the diffuse type with 13% DEGS. Furthermore, the lineage from metastasis showed 33% of DEGS up-regulated and 66% of DEGS down-regulated. Conclusions: Our study is the first to describe bioinformatics methods the effect before and after the silencing of the MYC gene in cell lines of gastric cancer northern people of Brazil. Our results showed that depending on the histological type there are many functional genes between the three strains that were recorded significantly associated with pathways enriched for cancer, metabolism, adhesion, cell cycle, proteolysis and signaling, suggesting the existence of routes of different carcinogenesis that lead normal mucosa to turn into gastric cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE81265 | GEO | 2016/05/10

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to investigate NGS-derived rice leaf transcriptome profiling (RNA-seq) exposed to green rice leafhopper (GRH) and validated RNA-Seq results using quantitative reverse transcription polymerase chain reaction (qRT–PCR). Methods: Rice leaf mRNA profiles of 21-day-old wild-type (WT) and Near Isogenic Line (NIL) rice were generated by deep sequencing, in triplicate, using Illumina’s HiSeq™ 4000 Sequencing System. For assembled genes, longest contigs of the assembled contigs were filtered and clustered into the non-redundant transcripts using CD-HIT-EST (Li et al., 2001; Bolger et al., 2014). qRT–PCR validation was performed using ROX and SYBR Green assays. Results: RNA-Seq results revealed that an average of 1,766,347 (1,240,317 in control and 526,030 GRH treated plants) and 3,676,765 (2,986,748 control and 690,017 GRH) counts per million mapped (CPM) reads were generated from Ilpum and NIL GRH treated plants, respectively. After alignment, more than 75% of all reads were successfully mapped to the reference genome, and 8,859 genes and 15,815,400 transcripts were obtained. GRH infestation caused differential expression of 4265 up-regulated and 4,594 down-regulated genes in Ilpum, while in NIL, 4,479 and 4,380 genes were up- and down-regulated, respectively 48 h post-infestation. A total of 3,424 differentially expressed genes (DEGs, 1,605 up-regulated in Ilpum and down-regulated in NIL; 1,819 genes up-regulated in NIL and down-regulated in Ilpum) were identified. Interestingly, these DEGs were found to be involved in key physiological processes, with interesting molecular functions, including plant defense against diverse biotic stresses, hormone signaling, and other developmental processes. Based on the quantile normalization of the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values followed by student’s t-test (p <0.05) we identified 3,283 DEGs in Ilpum (1,935 upregulated and 1,348 downregulated) and 2,599 DEGs in NIL (1,621 up-regulated and 978 down-regulated) with at least log2 (logarithm base 2) 2-fold change (Log2FC) in expression upon GRH infestation. Conclusions: The current study has provided the first RNA-Seq dataset and comparative transcriptome profile of GRH responsive genes from Ilpum (GRH-susceptible rice cultivar) and a near isogenic line (NIL) carrying Grh1 gene introduced from Shingwang into Ilpum to investigate the possible transcriptional interaction with other defense related genes. In addition, RNA-Seq data and MapMan analysis revealed the activation of multiple regulatory pathways following GRH infestation. Furthermore, the observed differential transcriptome profile between Ilpum and NIL would suggest the existence of a possible interaction network between Grh1 and other defense related genes towards GRH resistance in rice.

Project description:Purpose: Feeding larvae of fly models of polyQ and other neurodegenerative disorders on AR or RS supplemented food substantially suppressed neurodegeneration. With a view to gain further insight into the suppression of polyQ pathology by AR or RS, we expressed the UAS-127Q transgene using the predominantly eye-specific GMR-GAL4 driver and examined the transcriptomic changes in wild type and 127Q-expressing eye discs following feeding on AR or RS. In order to find out reason underlying the suppression of neurodegeneration by feeding of AR and RS, we checked difference in gene expression between eye discs expressing GMR-GAL4>UAS-127Q and wild type. Method: Eye disc RNA profiles of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads, 12 samples per lane and each sample run across 2 lanes of flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 19-25 million reads. The resulting sequencing fastq files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 19-25 million sequence reads per sample to the Drosophila melanogaster genome (dm6) and identified 15,904 transcripts with cufflink workflow in each genotypes studied. The GMR-GAL4 driven UAS-127Q expression in eye discs reared on AR supplemented food resulted in 259 differential expression, with 147 genes being down-regulated and 112 up-regulated, when compared with those reared on normal food, however, when larvae from same genotype reared on RS supplemented food resulted in 1641 DEGs, with 846 genes being down-regulated and 795 up-regulated compared with larvae reared on normal food. In eye disc of wild type larvae reared on AR supplemented food resulted in 680 DEGs, with 470 genes being down-regulated and 205 up-regulated compared with those reared on normal food. Larvae from wild type reared on RS supplemented food resulted in 427 DEGs, with 264 genes being down-regulated and 163 up-regulated compared with those reared on normal food. Compared to only GMR-GAL4>UAS-127Q and wild type larval eye discs reared on normal food, total of 1691, with 799 gene were up-regulated while 892 were down-regulated. Conclusion: The present results not only re-inforce earlier findings from our lab that the Ayurvedic Amalaki Rasayana and Rasa-Sindoor are potent suppressors of neurodegeneration but also provide direct evidence that these general health-promoting formulations significantly alter expression of many genes in protein-aggregation-clearance pathways and thus eliminate the cause of proteinopathy so that cell death is inhibited while other normal cellular activities continue. These formulations, which have been used in Ayurvedic practice for thousands of years as health-promoting as well as curative supplements, do not have any side-effects. Therefore, we believe that these Ayurvedic formulations have a good potential to ameliorate the sufferings of polyQ and other neurodegenerative disorders.

Dataset Information

Next-Generation Sequencing reveals the effects of MYC silencing in gastric cancer cell lines from northern Brazil

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets