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Cell-type, allelic and genetic signatures in the human pancreatic beta cell transcriptome

Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diabetes. Describing the differentiated state of the human beta cell has been hampered so far by technical (low resolution microarrays) and biological limitations (whole islet preparations rather than isolated beta cells). We circumvent these by deep RNA sequencing of purified beta cells from 11 individuals, presenting here the first characterization of the human beta cell transcriptome. Additionally, we perform the first comparison of gene expression profiles between beta cells, whole islets (N=7) and beta cell depleted islet preparations (N=5), revealing thus beta cell specific expression signatures. Finally, we combine this with whole-genome sequencing data for 7 of our donors, describing here the first set of genetic variants controlling inter-individual variability in beta cell gene expression.

Type: Transcriptome Analysis
Archiver: European Genome-phenome Archive (EGA)

1 Dataset 5 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000393	None	Illumina HiSeq 2000	30

Publications	Citations
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. Nica AC, Ongen H, Irminger JC, Bosco D, Berney T, Antonarakis SE, Halban PA, Dermitzakis ET. Genome Res 23: 2013 1554-1562	156
Analysis artefacts of the INS-IGF2 fusion transcript. Wernersson R, Frogne T, Rescan C, Hansson L, Bruun C, Grønborg M, Jensen JN, Madsen OD. BMC Mol Biol 16: 2015 13	7
Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets. Lawson R, Maret W, Hogstrand C. BMC Genomics 18: 2017 719	14
Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells. Thomsen SK, Raimondo A, Hastoy B, Sengupta S, Dai XQ, Bautista A, Censin J, Payne AJ, Umapathysivam MM, Spigelman AF, Barrett A, Groves CJ, Beer NL, Manning Fox JE, McCarthy MI, Clark A, Mahajan A, Rorsman P, MacDonald PE, Gloyn AL. Nat Genet 50: 2018 1122-1131	72
Glucose-dependent partitioning of arginine to the urea cycle protects β-cells from inflammation. Fu A, Alvarez-Perez JC, Avizonis D, Kin T, Ficarro SB, Choi DW, Karakose E, Badur MG, Evans L, Rosselot C, Bridon G, Bird GH, Seo HS, Dhe-Paganon S, Kamphorst JJ, Stewart AF, James Shapiro AM, Marto JA, Walensky LD, Jones RG, Garcia-Ocana A, Danial NN. Nat Metab 2: 2020 432-446	51