Omics · study · 2026
A single chromosome 3p break initiates clear cell renal cell carcinoma evolution
Listed in NCBI GEO
We used single-cell RNA sequencing (10x Genomics) coupled with CITE-seq cell hashing (HTO) to profile and compare the transcriptomes of renal proximal tubule epithelial cells (RPTECs) after different CRISPR-Cas9 ribonucleoprotein (RNP) perturbations.
Description
Cells were treated with a non-targeting control sgRNA (sgNTC), an sgRNA targeting chromosome 3p (sg3p), or an sgRNA targeting chromosome Yq (sgYq), and harvested at Day 5 and Day 10.
Hashtag-labeled samples were pooled into three 10x Chip G lanes, and gene-expression and HTO libraries were sequenced on an Illumina NovaSeq X Plus. Copy-number alterations were inferred (inferCNV) to identify cells with chromosome 3p loss, and differential gene expression was compared between 3p-loss and no-loss populations over time.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE336nnn/GSE336056 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE336056 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1480644 ncbi.nlm.nih.gov/bioproject/PRJNA1480644 ↗
project · from NCBI GEO
- PubMed 42465403 pubmed.ncbi.nlm.nih.gov/42465403 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens · Other
- From keywords
- Life Sciences
- Inferred from text
- Genetics 69% · RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 75%
Related
- Possibly the same asA single chromosome 3p break initiates clear cell renal cell carcinoma evolution
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE336056 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:group:3105 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (69%) |
| 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[method].geo_series_type:other | 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[modality].local:modality:single-cell-rna-seq | 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 |