Omics · study · 2026
RNA-seq of SW620 colorectal cancer cells: control (sh-control) versus ANO1 (TMEM16A) knockdown (sh-ANO1)
Listed in NCBI GEO
The calcium-activated chloride channel ANO1 (TMEM16A) is overexpressed in colorectal cancer (CRC) and associated with poor prognosis, but its role in regulating metastatic plasticity is not fully understood.
Description
To elucidate the transcriptomic networks governed by ANO1, we performed RNA sequencing on SW620 CRC cells stably expressing sh-control or sh-ANO1. Total RNA was extracted using Trizol reagent.
Sequencing libraries were constructed with the NEBNext® Ultra RNA Library Prep Kit for Illumina® and sequenced on an Illumina Novaseq platform, generating 125-150 bp paired-end reads. Bioinformatics analysis included read alignment with HISAT2 (v2.0.5) and differential expression analysis using DESeq2 (v1.20.0) with a threshold of |log2(Fold Change)| ≥ 1 and adjusted p-value < 0.05. Functional enrichment analysis for Gene Ontology (GO) and KEGG pathways was performed with clusterProfiler (v3.8.1).
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Gene Set Enrichment Analysis (GSEA) was conducted using gene sets from MSigDB. Transcriptomic profiling identified 1,894 differentially expressed genes (DEGs) upon ANO1 knockdown, with 1,523 downregulated and 371 upregulated. Downregulated genes included key EMT and signaling components (e.g., PIK3C2A, PIK3CA, KRAS, ZEB1).
GO analysis revealed enrichment in processes related to genomic integrity and cell division. KEGG pathway analysis highlighted significant enrichment in “Homologous recombination” and “Platinum drug resistance”. A trend-level downregulation was observed for the “mTOR signaling pathway”.
This dataset illustrates that ANO1 knockdown drives broad changes in a pro-metastatic transcriptome network and implicates mTOR signaling as a potential downstream mechanism, providing a resource for understanding how ANO1 promotes CRC progression.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE310nnn/GSE310994 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE310994 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1367911 ncbi.nlm.nih.gov/bioproject/PRJNA1367911 ↗
project · from NCBI GEO
- PubMed 42144424 pubmed.ncbi.nlm.nih.gov/42144424 ↗
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 75% · Sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE310994 | 14 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 (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| 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 |