Omics · study · 2026
RNA-seq of MDA-MB-231 with BCSC state sorting (A-BCSCs vs Q-BCSCs via SDorm system) and ENO1 silencing (siENO1 vs siNC)
Listed in NCBI GEO
Quiescent breast cancer stem cells (Q-BCSCs) can switch to an activated state (A-BCSCs).
Description
We established a dual-reporter system for stemness and quiescence (NANOG-EGFP + H2B-mCherry pulse-chase) to isolate A-BCSCs and Q-BCSCs from MDA-MB-231 cells. Strand-specific poly(A) RNA-seq was performed to compare A-BCSCs vs Q-BCSCs (n=3 per group).
In a second dataset, ENO1 silencing (siENO1) was compared with a non-targeting control (siNC) in unsorted MDA-MB-231 cells (n=2 per group). Processed data are provided as separate experiment-specific gene-level matrices rather than a single unified matrix because different Ensembl gene annotation releases were used for quantification in the two experiments. For the A-BCSCs vs Q-BCSCs dataset, counts and FPKM matrices together with a matching gene annotation table are provided.
Read the rest (2 more)
For the siENO1 vs siNC dataset, counts and FPKM matrices together with a matching gene annotation table are provided. Previous reports have identified NANOG as a key stemness factor in tumor cells. Based on this, we established a stable fluorescent reporter system in MDA-MB-231 cells via lentiviral transduction, in which EGFP is driven by the NANOG promoter and expressed upon NANOG activation.
To validate whether this system faithfully reflects cellular stemness, NANOG-EGFP positive and negative cells were sorted by FACS and subsequently analyzed by RNA-seq. Our results showed that the NANOG-EGFP positive population was enriched for stemness-related gene pathways, confirming that this reporter system can effectively indicate tumor cell stemness
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE309nnn/GSE309470 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE309470 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1335094 ncbi.nlm.nih.gov/bioproject/PRJNA1335094 ↗
project · 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% · Tabular 65%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE309470 | 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 (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[modality].local:modality:tabular | 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 |