Processed single-nucleus multiome objects and regulatory network analysis of MCF7 cells under acute acidosis, chronic acid adaptation, and return to physiological pH
Year: 2026
Type: dataset
Abstract: Processed objects and result tables for the single-nucleus multiome (snRNA-seq + snATAC-seq) analysis of MCF7 cells under four conditions (Control, Acute, Chronic, Return). Files are prefixed by the pipeline step that produced them: 00-2, integrated Seurat/Signac object after QC, MACS3 peak calling, SCT/LSI/WNN, clustering and chromVAR (41,355 nuclei); 01, hdWGCNA metacells and expression matrices; 02, ARACNe3 regulatory networks (rerun and original); 03, VIPER regulon and activity; 04, sphingolipid axis scores and diversity; 05, msVIPER candidate regulators per axis; 06, chromVAR deviations of the candidate regulators. All files except the original ARACNe3 network were generated by the code at https://github.com/StudyingAnt/SL_plasticity_acidosis_snMultiome from the Cell Ranger ARC outputs in GEO (GSE352076). MD5 checksums are in md5sums.txt.
Authors: Chalar, Raafat, Khatri, Naheel, Obeid, Jowana, Song, Joon-Hyun, Xiao, Yujie, Samad, Saiful, Chen, Andrew, Resnick, Andrew, Karbalaei, Khadijeh, Ghandour, Botheina, Allopenna, Janet J., Medatwal, Nihal, Mao, Cungui, Clarke, Christopher, Velazquez, Fabiola, Chen, Bo, Luberto, Chiara, Canal, Daniel, Hannun, Yusuf, Damaghi, Mehdi
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7224417009