Omics · study · 2026
Effects of 3D and 2D culture on gene expression of HCT116 cells
Listed in NCBI GEO
Accurate preclinical models that recapitulate in vivo tumor pathophysiology are essential for reliable assessment of anticancer drug efficacy.
Description
Three-dimensional (3D) cell culture systems, which better mimic the in vivo microenvironment, have garnered significant attention. However, high throughput production of uniformly sized spheroids remains a key challenge for drug screening. we developed a PDMS substrate with hexagonally arrayed U-shaped microwells (HAUM PDMS) for high-throughput culture of uniformly sized spheroids.
Transcriptome sequencing was performed on HCT116 spheroids harvested from 500 µm HAUM PDMS substrates and on 2D-cultured cells after 3 days. The results showed that transcriptome analysis indicated that up-regulated genes in spheroids were mainly related to cell division and proliferation.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE344nnn/GSE344100 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344100 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1514613 ncbi.nlm.nih.gov/bioproject/PRJNA1514613 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Biochemistry and cell biology 72% · Cancer 65% · RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE344100 | 13 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 (65%) |
| concepts[field].anzsrc:group:3101 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (72%) |
| 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[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 |