Dataset Information

A transcriptomic and proteomic map of primary human cell types

ABSTRACT: Molecular profiling of human primary cell types is essential for a comprehensive understanding of human biology. Here, we describe the transcriptome and proteome map of 28 primary human cell types. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed at both the transcriptome and proteome levels along with the discovery of cell type specific molecules including GRAP and C1orf116. Among them, we further validated the expression of a novel epithelial cell specific protein C1orf116 using immunohistochemistry across a range of human tissues. An exhaustive protein database search considering 39 different post-translational modifications (PTMs) provided new insights into the PTM landscape of primary cells. This approach enabled the identification of previously understudied PTMs such as serine O-acetylation and histidine methylation, while also providing comprehensive characterization of proteins with diverse PTM types. Interestingly, the unexpectedly higher frequency of dioxidation on tryptophan compared to methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria. Further, a unique protein database search strategy that considered alternative translational start sites, splice junctions and translational readthrough provided an opportunity to refine genome annotation using proteomic evidence. As an example, several peptides derived from translational readthrough were detected including extended sequence of LDHB and MDH1, which is the first report with peptide level evidence for these proteins. We believe that our data with an extensive catalog of the transcriptome and proteome of normal human primary cells will provide unique insights into cell biology revealing cellular heterogeneity and cell type-specific molecular cues. These insights could have a broad impact of pathophysiology of disease mechanisms that were missed by tissue proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Primary Cell

SUBMITTER: Akhilesh Pandey

LAB HEAD: Akhilesh Pandey

PROVIDER: PXD062642 | Pride | 2026-01-23

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	AoSMC_CellMap_SCX_r1_f01.raw	Raw
	AoSMC_CellMap_SCX_r1_f02.raw	Raw
	AoSMC_CellMap_SCX_r1_f03.raw	Raw
	AoSMC_CellMap_SCX_r1_f04.raw	Raw
	AoSMC_CellMap_SCX_r1_f05.raw	Raw

Items per page:

1 - 5 of 508

Publications

A transcriptomic and proteomic map of primary human cell types.

Mun Dong-Gi DG Madugundu Anil K AK Renuse Santosh S Nirujogi Raja Sekhar RS Na Chan Hyun CH Kim Min-Sik MS Saraswat Mayank M Singh Smrita S Ramarajan Madan G MG Tiwary Shivani S Cox Jürgen J Prakash Amol A Halushka Marc K MK Burns Kathleen H KH Kandasamy Richard K RK Pandey Akhilesh A

Nucleic acids research 20260101 2

Molecular profiling of human primary cell types is essential for understanding human biology. We present a transcriptome and proteome map of 28 primary human cell types. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed in both the transcriptome and proteome levels along with the discovery of cell type enriched molecules including GRAP and C1orf116. The epithelial cell specific protein C1orf116 was further validated using immunohistochemistry across variou ...[more]

PMID: 41533574

Similar Datasets

Project description:Molecular profiling of human primary cell types is essential for holistic understanding of human biology. Here we present a map of 28 human primary cell types with comprehensive measurements of expressed transcripts and proteins. Three major clusters of epithelial, endothelial, and mesenchymal cell types were observed both at transcriptome and proteome level along with discovery of several cell type specific proteins. Among them, we characterized the novel epithelial specific protein C1orf116 which was further validated with immunohistochemistry across various human tissues. Comprehensive proteome profiling across cell types allowed characterization of ten orphan proteins including TMEM252 and TM4SF18 which lacked protein level evidence. Exhaustive protein database search considering 27 biologically relevant post-translational modifications and 12 chemical modifications was performed, thanks to the increased performance of cloud-based search engine. This, for the first time, provided the catalog of post-translational modifications across cell types, which serve as a resource of PTMs for future studies. We characterized proteins such as protein EEF1A1with various types of PTMs and understudied PTMs including histidine methylation, and O-acetylation of serine. Interestingly, the unexpected higher frequency of dioxidation on tryptophan than that of methionine led us to characterize oxidative mitochondria complex subunit proteins modified through oxidative phosphorylation in mitochondria, which was mostly considered as chemical artifact so far. Overall, these indicated that considering various PTMs during protein database search from non-enriched samples could be routinely used in proteomics experiments. Further, protein database search strategy considering alternative translational start sites, splice junctions, and translational readthrough provided a unique opportunity to refine genome annotation with their proteomic evidence. We believe that our data with the large catalog of transcriptome and proteome of normal human primary cells provide a cornerstone for holistic understanding of cell biology.

Project description:Background: MicroRNAs (miRNAs) are short non-coding RNAs predicted to regulate one third of protein-coding genes via mRNA targeting. In conjunction with key transcription factors, such as the repressor REST (RE1 silencing transcription factor), miRNAs play crucial roles in neurogenesis, which requires a highly orchestrated program of gene expression to ensure the appropriate development and function of diverse neural cell types. Whilst previous studies have highlighted select groups of miRNAs during neural development, there remains a need for amenable models in which miRNA expression and function can be analyzed over the duration of neurogenesis. Principal Findings: We performed large-scale expression profiling of miRNAs in human NTera2/D1 (NT2) cells during retinoic acid (RA)-induced transition from progenitors to fully differentiated neural phenotypes. Our results revealed dynamic changes of miRNA patterns, resulting in distinct miRNA subsets that could be linked to specific neurodevelopmental stages. Moreover, the cell-type specific miRNA subsets were very similar in NT2-derived differentiated cells and human primary neurons and astrocytes. Further analysis identified miRNAs as putative regulators of REST, as well as candidate miRNAs targeted by REST. Finally, we confirmed the existence of two predicted miRNAs; pred-MIR191 and pred-MIR222 associated with SLAIN1 and FOXP2, respectively, and provided some evidence of their potential co-regulation. Conclusions: In the present study, we demonstrate that regulation of miRNAs occurs in precise patterns indicative of their roles in cell fate commitment, progenitor expansion and differentiation into neurons and glia. Furthermore, the similarity between our NT2 system and primary human cells suggests their roles in molecular pathways critical for human in vivo neurogenesis. The experiment consists of a total of 51 arrays: 29 retinoic acid time series arrays (0,2,4,6,8,12,14,21 and 28 days), 2 each of NT2-derived neurons and astrocytes, 12 primary human fetal astrocytes, 3 primary human embryonic astrocytes and 3 primary human neurons. Each condition has a minimum of 2 biological replicates. The samples were compared as single channel experiments. NOTE: The raw data files were submitted as generated in Quantarray with 2 channels, but due to issues with the control sample dye (Cy5 on Channel 1), only the Channel 2 (Cy3) data was analysed.