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Series GSE223181 Query DataSets for GSE223181
Status Public on Sep 27, 2023
Title Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remains underexplored. Using ATAC-sequencing and RNA-sequencing, we characterized differences in chromatin accessibility and gene expression between EA-derived versus AA-derived TNBC cell lines (N=9). Our analyses revealed significant differences in transcription factor binding and downstream gene expression associated with cancer stemness, resistance, and epithelial to mesenchymal transition. Differences were exacerbated under conditions of hypoxia. Together, these data suggest a differential chromatin and transcriptomic landscape that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. 
 
Overall design RNA was isolated from breast cancer cell lines (n = 8 normoxia and n = 8 hypoxia) using TRIzol method. The mRNA profiles of the above breast cancel cell lines were generated by deep sequencing using Illumina  NextSeq 2000  P2.
 
Contributor(s) Harris AR, Panigrahi G, Liu H, Koparde V, Bailey-Whyte M, Dorsey TH, Yates C, Ambs S
Citation(s) 37732899
Submission date Jan 18, 2023
Last update date Oct 19, 2023
Contact name Stefan Ambs
E-mail(s) ambss@mail.nih.gov
Phone 240-760-6836
Organization name NCI
Department CCR
Lab LHC
Street address Building 37, Room 3050B
City Bethesda
State/province MD
ZIP/Postal code 20892-4258
Country USA
 
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (16)
GSM6940687 1_Dorsey
GSM6940688 2_Dorsey
GSM6940689 3_Dorsey
This SubSeries is part of SuperSeries:
GSE223183 Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry
Relations
BioProject PRJNA925294

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Supplementary file Size Download File type/resource
GSE223181_RawCountFile_rsemgenes.txt.gz 1.2 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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