Omics · study · 2026
Single-cell transcriptomic effects of LOX knockdown on tumor cell xenografts implanted on aged mouse breast dECM scaffolds
Listed in NCBI GEO
We profiled the single-cell transcriptomic effects of LOX (lysyl oxidase) knockdown on MCF10DCIS.com human breast tumor cells and on CD11b+ tumor-associated myeloid cells in an aged-microenvironment xenograft model.
Description
GFP-reporting MCF10DCIS.com cells transduced with either pLKO empty-vector (control) or pLKO-LOX shRNA were seeded onto decellularized/delipidized breast dECM scaffolds derived from aged C57BL/6 mice, cultured for 12 days, and implanted bilaterally into Rag1-/- (B6.129S7-Rag1tm1Mom/J) host mice (right flank = pLKO ctrl, left flank = shLOX, matched within-mouse pairing).
Tumors grew for 7 weeks. Three biological replicate pairs (n=3 pLKO + n=3 shLOX, from 3 host mice) were selected for Parse Biosciences Evercode WT v2 single-cell RNA-seq. Each tumor was dissociated and split into a CD11b- tumor-cell fraction and a CD11b+ tumor-associated myeloid fraction, yielding 12 biological samples total (6 tumor + 6 immune).
Read the rest (1 more)
All 12 samples were combinatorially barcoded together and split into 8 sublibraries. Deposited FASTQs are per-biological-sample read groups: after split-pipe v1.0.6p combinatorial demultiplexing, reads were partitioned by assigned sample identity and concatenated across all 8 sublibraries and both sequencing runs, producing one R1/R2 pair per biological sample.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE333nnn/GSE333415 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE333415 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1471051 ncbi.nlm.nih.gov/bioproject/PRJNA1471051 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Homo sapiens · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Cancer 65% · RNA sequencing 65% · Sequencing 75% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE333415 | 12 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].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[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| 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 |