HCA Data Explorer

Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia

Updated April 4, 2023

During tumour growth cancer cells are subject to and selected by microenvironmental stress. The selection of such cells allows for continued growth and survival, during hypoxia, acidosis, nutritional deprivation, drug treatment and radiation. However, there is great microenvironmental heterogeneity in every tumour. Must studies of gene regulation in vitro investigate whole cell populations, often by western blotting or mRNA expression. Thus, the individual variability of gene induction that could lead to selection, and basal cell molecular variability on which the selection operates, basic Darwinian principles, are not defined. We previously showed that two distinct populations can often be induced in epithelial tumour cell lines under hypoxia, identified by induction of Carbonic Anhydrase 9 [CA9].Here, we investigated the heterogeneity of breast cancer cells, and the relationship to the CA9 positive population in hypoxia, by using single cell sequencing analysis. Overall design: Examination of the MCF7 breast cancer cell line using single cell transcriptomics (smartseq2)

Adam P CribbsUniversity of Oxfordadam.cribbs@ndorms.ox.ac.uk
Adam P Cribbs (Experimental Scientist)1
1University of Oxford
Parisa Nejad

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/f6133d2a-9f3d-4ef9-9c19-c23d6c7e6cc0
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Analysis Portals

None

Project Label

THP1StimulationCells

Species

Homo sapiens

Sample Type

cellLines

Anatomical Entity

breast

Organ Part

mammary gland

Selected Cell Types

epithelial cell

Model Organ

breast

Disease Status (Specimen)

adenocarcinoma

Disease Status (Donor)

breast cancer

Development Stage

human adult stage

Library Construction Method

Smart-seq2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5

File Format

5 file formats

Cell Count Estimate

384

Donor Count

1
bai384 file(s)bam384 file(s)fastq.gz384 file(s)loom1 file(s)xlsx1 file(s)