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| Status |
Public on May 10, 2016 |
| Title |
Next-Generation Sequencing reveals the effects of MYC silencing in gastric cancer cell lines from northern Brazil |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
It was help silencing MYC in three lines of gastric cancer, originating from diffuse and intestinal histologic types and the third of a metastasis from a stomach tumor originating in a ascites. These three cell lines were subjected to sequencing semiconductor Pronton Ion before and after the silencing of MYC.
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| Contributor(s) |
Burbano RR, Jersey M, Caroline M, Hellen R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJEB7457 |
| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Carvalho |
| E-mail(s) |
suporte@genone.com.br
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| Organization name |
GenOne Biotetechnologies
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| Street address |
Caixa Postal 26820
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| City |
Rio de Janeiro |
| State/province |
Rio de Janeiro |
| ZIP/Postal code |
21875-970 |
| Country |
Brazil |
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| Platforms (1) |
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| Samples (6)
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| GSM2147866 |
Samples treated with control siRNA [1C] |
| GSM2147867 |
Sample siRNA against the MYC gene [1M] |
| GSM2147868 |
Samples treated with control siRNA [2C] |
| GSM2147869 |
Sample siRNA against the MYC gene [2M] |
| GSM2147870 |
Samples treated with control siRNA [3C] |
| GSM2147871 |
Sample siRNA against the MYC gene [3M] |
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| Relations |
| SRA |
ERP007187 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81265_1C-VS-1M.GeneDiffExp.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE81265_2C-VS-2M.GeneDiffExp.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE81265_3C-VS-3M.GeneDiffExp.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| GSE81265_RAW.tar |
1.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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