Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single-cell RNA-seq and CITE-seq of autochthonous KP and KPN mouse tumors

ABSTRACT: Colorectal cancers are complex ecosystems, with interactions between the cancer epithelium and the tumor microenvironment (TME) shaping disease progression. Cancer-associated fibroblasts are key TME components, influencing epithelial plasticity and immune cell infiltration. In this study, we collected autochthonous tumours from KP (villinCreER KrasG12D/+ Trp53fl/fl) and KPN (villinCreER KrasG12D/+ Trp53fl/fl Rosa26N1icd/+) mice, colorectal cancer models that develop invasive tumours and metastasise to the liver with high penetrance and short latency. We aimed to characterise the cellular composition of these tumours, focusing on shifts in different cell compartments, particularly fibroblast phenotypes. Dissociated single cells were enriched for fibroblasts by fluorescence-activated cell sorting based on negative expression of Epcam and Cd45 (Double negative, DN). Single-cell RNA sequencing and CITE-seq were performed. CITE-seq staining used the TotalSeq™-C Mouse Universal Cocktail V1.0 (BioLegend), and cell hashing was performed using TotalSeq™-C0308 anti-mouse Hashtag 8 (Barcode: TATAGAACGCCAGGC) and TotalSeq™-C0314 anti-mouse Hashtag 14 (Barcode: CTTTCGCCAACTCTG).

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Mus musculus

SUBMITTER: Muyang Lin

PROVIDER: E-MTAB-15841 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:We examined the transformation susceptibility of different cerebellar stem/progenitors by developing several new Group3 medulloblastoma murine models using orthotopic transplantation and in utero electroporation (EP)-based in vivo gene transfer with Cre/LoxP-mediated conditional Myc gene activation and loss of Trp53 function. We used microarrays to compared the transcriptome of these novel Group3 medulloblastoma mouse models to existing mouse models of medulloblastoma subgroups and used cross-species analysis to compare these models to human medulloblastoma subgroups This study aimed to investigate the cell of origin of Group3 MB using our orthotopical MYC model followed by a novel electroporation approach. Orthotopic cell-lineage specific MYC tumors were generated by enforced Myc expression in P6 GNPs isolated from P0-1 tamoxifen treated [Atoh1-CreER;Trp53fl/-] and [Prom1-CreER;Trp53fl/-] mice followed by cortical implants in immunocompromised mice. These tumors are referred to as Atoh1ER-MYC [dka072-075], Prom1-CreER [dka077-081]. The first Group3 MB models in which tumors developed in situ were generated by electroporation of plasmids containing Myc and dominant negative Trp53 flanked by loxP sites into the fourth ventricle of E13.5 Blbp-Cre [dka081, 087, 089, 090, 091 and blm121], Gad2-IRES-Cre [blm128-130 and blm134] and Ptf1a-Cre [blm135-137] mouse embryos. The gene expression profile of these tumors were compared to our previously published Group3 MB model as well as SHH and WNT models of medulloblastoma. For SHH subgroup medulloblastoma, [dka001-005, 009, 033 and 034] and [dka050-057], spontaneous medulloblastomas from [Cdkn2c-/-; Trp53Fl/Fl; Nestin-Cre] and [Cdkn2c-/-; Ptch1+/-] (Uziel et al.,2005 Genes Dev) were used, respectively. For Group3 medulloblastomas, [dka013-16, 049 and 065-067], in which Myc was overexpressed in Cdkn2c-/-, Trp53-/- cerebellar cells and implanted into the cortices of immunocompromised nude mice prior to tumor isolation. For WNT subgroup medulloblastomas [pgr003, 016 and 066], spontaneously developed tumors from CTNNB1+/lox (ex3); BLBP-Cre; Trp53Fl/Fl (Gibson et al., 2010, Nature) were removed for RNA extraction.

Dataset Information

Single-cell RNA-seq and CITE-seq of autochthonous KP and KPN mouse tumors

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets