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Series GSE172155 Query DataSets for GSE172155
Status Public on Aug 16, 2021
Title SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies such as CITE-seq have been developed that enable simultaneous quantitative analysis of cell-surface receptor expression with transcriptional states. To date, these datasets have not been used to systematically develop cell-context-specific maps of the interface between signaling and transcriptional regulators orchestrating cellular identity and function. We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to immune cell types in the blood to predict the coupling of signaling receptors with cell context-specific TFs. The predictions are validated by prior knowledge and flow cytometry analyses. SPaRTAN is then used to predict the signaling coupled TF states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN greatly enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states.
Overall design Human malignant mesotheliomas were profiled using CITE-seq
Web link
Contributor(s) Osmanbeyoglu HU, Somasundaram A, Qi Z, Ma X
Citation(s) 34500467
Submission date Apr 15, 2021
Last update date Jan 11, 2022
Contact name Hatice Ulku Osmanbeyoglu
Phone 4126237789
Organization name University of Pittsburgh
Department Biomedical Informatics
Lab Osmanbeyoglu Lab
Street address 5117 Centre Ave. G27c
City Pittsburgh
State/province Pennsylvania
ZIP/Postal code 15213
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (4)
GSM5242790 Gene expression from malignant pleural mesothelioma patient
GSM5242791 Antibody-derived tags from malignant pleural mesothelioma patient
GSM5242792 Gene expression from malignant peritoneal mesothelioma patient
BioProject PRJNA722248
SRA SRP314970

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE172155_mpem_barcodes.tsv.gz 24.7 Kb (ftp)(http) TSV
GSE172155_mpem_features.tsv.gz 298.1 Kb (ftp)(http) TSV
GSE172155_mpem_matrix.mtx.gz 23.5 Mb (ftp)(http) MTX
GSE172155_mpm_barcodes.tsv.gz 34.3 Kb (ftp)(http) TSV
GSE172155_mpm_features.tsv.gz 298.0 Kb (ftp)(http) TSV
GSE172155_mpm_matrix.mtx.gz 41.7 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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