Dataset Information

Proteomic Profiling of Kidney Organoids in Extended Culture Conditions

ABSTRACT: We conducted a global proteomics analysis on kidney organoids at three distinct culture time points: day 22, day 33, and day 38. Our objective wasto investigate the impact of extended culture, beyond the standard differentiation endpoint of day 21, on the organoid protein expression profile.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Stem Cell, Kidney

DISEASE(S): X-linked Alport Syndrome

SUBMITTER: Hassan Saei

LAB HEAD: Corinne Antignac

PROVIDER: PXD057360 | Pride | 2025-10-28

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20240423_LennonR_HassanS_d22_ECM_R1.raw	Raw
	20240423_LennonR_HassanS_d22_ECM_R1_cond.raw	Raw
	20240423_LennonR_HassanS_d22_ECM_R2.raw	Raw
	20240423_LennonR_HassanS_d22_ECM_R3.raw	Raw
	20240423_LennonR_HassanS_d22_ECM_R3r.raw	Raw

Items per page:

1 - 5 of 22

Similar Datasets

Project description:Background: Germ Cell Cancers (GCC), originating from Primordial Germ Cells /gonocytes, are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS, stem cell component: embryonal carcinoma (EC)). Somatic mutations are rarely found in GCC. It has been proposed that disruption of the epigenetic constitution, either primarily or secondary (e.g. environmental influences), is involved in cancer, and specifically in GCC. Results: This study aims at identifying epigenetic footprints of SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in GCC and related disruption of germ cell maturation. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data was acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP sequencing (activating histone modifications (H3K4me3, H3K27ac)). The data show that known germ cell markers are not only present and differentiating between SE and NS at the expression level, but also in the epigenetic landscape. Conclusion: The overall similarity between TCam-2 / NCCIT supports an erased embryonic gem cell arrested in early gonadal development as common origin. Subtle difference in the (integrated) epigenetic and expression profiles indicated TCam-2 to exhibit a more germ cell like profile (enrichment Androgen regulation) while NCCIT proved more pluripotent. The results provide insight into an integrated analysis of the functional genome in GCC cell lines. Two wildtype germ cell cancer (type II germ cell tumor) cell lines were analyzed. TCam-2 (representative for the seminomatous subtype of germ cell cancer) , [1, 2]) and NCCIT (representative of the non-seminomatous (embryonal carcinoma) subtype of germ cell cancer, [3]). Of each cell line two biological replicates were included. Genomic positions reported are based on the GRch37/hg19 assembly. 1. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8. 2. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96. 3. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.

Dataset Information

Proteomic Profiling of Kidney Organoids in Extended Culture Conditions

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets