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High-throughput sequencing of oxidative stress for Human gastric cancer cell lines treatment with Bioactive polypeptide chelating selenium (ACBP-S-Se)

GSE173219 Homo sapiens (human) Non-coding RNA profiling 2 samples Submitted 2024/04/23 Platform GPL20301
At a glance

Non-coding RNA profiling · human · 2 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Homo sapiens (human)
Topic
Gastric cancerThis series is part of our curated briefing on it.
Samples
2 samples
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
The functional gene analyses revealed 911 upregulated genes and 1122 downregulated genes after ACBP-S-Se treatment in MKN-45 cells. From the functional enrichment analyses of oxidative stress-related genes, a total of 75 genes with significant differences were selected .
Read the full summary ↓
From the gene interaction mapping, CDKN1A, CCNB1, TXN and MAP3K5 were extracted due to the roles of most genes with which they associate and to the significantly enriched pathways, which can be used as downstream molecules.according to the interaction of genes related to oxidative stress and lncRNAs, networks of oxidative stress genes and lncRNA interactions (lncRNA FPKM>5) were constructed via lncRNA trans and cis analysis (TRANS_ENERGY<-50). The results showed that the network contained 55 genes related to oxidative stress and 37 lncRNAs.The selected lncRNAs included MSTRG.13268.2, ENST00000508832, ENST00000580180, ENST00000454068, ENST00000607476,ENST00000504539, ENST00000326677, ENST00000448718, ENST00000531126 and MSTRG.5031.1.the expression of oxidative stress-related genes (the 4 selected genes) in The Cancer Genome Atlas (TCGA) and the expression of CDKN1A was increased after treatment with ACBP-S-Se, but the expression of this gene was lower in tumor samples than in paracancerous samples. The expression of the other three genes was decreased after treatment with ACBP-S-Se but was lower in tumor samples than in paracancerous samples.
This dataset
Open GSE173219 in finder → Find more human RNA-seq datasets → Gastric cancer landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE173219_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

Also filed as BioProject PRJNA724713 and SRA study SRP316067. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Samples in this study

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