Omics · study · 2026
Effects of EGCG, resveratrol and their combination on gene expression
Listed in NCBI GEO
Natural products available in vegetables, fruits and spices have drawn great deal of attention because of their chemopreventive potential.
Description
The purpose of this RNASeq experiment is to investigate the effect of two natural compounds EGCG and reveratrol and their combination on gene expression. Head and neck cancer cell line MDA686TU was treated with 40 μM EGCG, 15 μM resveratrol and their combination for 24 h.
Total RNA was used for RNASeq. RNASeq libraries were sequenced in a 2 × 50 paired-end design on an Illumina HiSeq1500. Raw reads were imported from the Illumina HiSeq1500 using bcl2fastq2 v2.17.1.14 (Illumina) and trimmed to remove adapter content and low-quality base calls, with reads trimmed to a length of less than 25 bases removed from further analysis using Trimmomatic v0.36.
Read the rest (1 more)
Quality of reads was assessed before and after trimming using FastQC v0.11.5 (Babraham Institute, Cambridge, England). Reads were aligned to the human reference genome GRCh38 using HISAT2 v2.0.4, and the resulting bam files were sorted and indexed using SAMtools v 1.3.1. DESeq2 was used to identify differentially expressed genes (DEG) with a False Discovery Rate (FDR) threshold of 0.1.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE305nnn/GSE305867 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE305867 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1308052 ncbi.nlm.nih.gov/bioproject/PRJNA1308052 ↗
project · from NCBI GEO
- PubMed 41976320 pubmed.ncbi.nlm.nih.gov/41976320 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Cancer 75% · RNA sequencing 65%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE305867 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |