RNA sequencing from patient-derived intestinal organoids

RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

Type: Transcriptome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD50000000492	uman duodenal tissues for establishing organoid cultures used in this study were sourced from de-identified surgical specimens (n = 3) of the duodenum obtained from patients who had undergone biopsy procedures unrelated to CeD at Tampere University Hospital. The protocol was approved by the Ethics Committee of Tampere University Hospital, Tampere, Finland (ETL code R18082). RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.	Illumina NovaSeq 6000	11

Publications	Citations
Transcriptomic analysis of intestine following administration of a transglutaminase 2 inhibitor to prevent gluten-induced intestinal damage in celiac disease. Dotsenko V, Tewes B, Hils M, Pasternack R, Isola J, Taavela J, Popp A, Sarin J, Huhtala H, Hiltunen P, Zimmermann T, Mohrbacher R, Greinwald R, Lundin KEA, Schuppan D, Mäki M, Viiri K, CEC-3 Investigators. Nat Immunol 25: 2024 1218-1230	0