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CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

ABSTRACT: Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their similarity to equivalent endogenous cell types. Single-cell and single-nucleus RNA sequencing (RNA-seq) are useful to gain such understanding, but they are expensive and time consuming, while bulk RNA-seq data can be generated quicker and at lower cost. In silico cell type decomposition is an efficient, inexpensive, and convenient alternative that can leverage bulk RNA-seq to derive more fine-grained information about these cultures. We developed CellMap, a computational tool that derives cell type profiles from publicly available single-cell and single-nucleus datasets to infer cell types in bulk RNA-seq data from iPSC-derived cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE174379 | GEO | 2023/01/01

REPOSITORIES: GEO

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Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and diseasee. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Here, we deeply profiled lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development and integrated this resource to analyze the transcriptomes of single cells. While lncRNAs were generally detected at low levels in whole tissues, single cell transcriptomics revealed that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Furthermore, we used CRISRPi to show that LOC646329, a lncRNA enriched in radial glia but detected at low abundance in tissues, regulates cell proliferation. The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types. 16 Bulk Tissue Samples from GW13-23; 226 Single Cells from GW19.5-23.5 ------------------ bulk_tpm.polya.txt: bulk RNA-seq expression; using polyA full reference scell_ncounts.genes.thresh.txt: single cell RNA-seq expression; using polyA stringent reference; includes 50 GW16, GW21, GW21p3 cells previously analyzed (Pollen et. al. 2014) polya_RNA_stringent_ref.gtf: bulk RNA-seq polyA stringent transcriptome reference polya_RNA_full_ref.gtf: bulk RNA-seq polyA full transcriptome reference total_RNA_stringent_ref.gtf: bulk RNA-seq total stringent transcriptome reference total_RNA_full_ref.gtf: bulk RNA-seq total full transcriptome reference GW13_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW13_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW14.5_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW16_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW21_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_1_total_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_polya_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_polya_plus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_total_minus.bw: strand-specific bulk RNA-seq alignment signal GW23_2_total_plus.bw: strand-specific bulk RNA-seq alignment signal

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CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

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