A proteogenomic atlas of the human neural retina

The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing factors. However, this technique provides limited information about transcript isoforms. To gain a deeper understanding of the human neural retina and its isoforms, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass-spectrometry and whole-genome sequencing data from three healthy human neural retina samples. About one third of the nearly 60,000 transcript isoforms were novel, and ten novel peptides that confirmed novel isoforms were detected. This study highlights the importance of studying tissue-specific transcriptomes in greater detail to better understand tissue-specific regulation and to identify disease-causing variants.

Type: RNASeq
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 1 Publication

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
EGAD50000000101	Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Files are raw BAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.	Sequel II	4
EGAD50000000720	Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Three PacBio libraries were prepared according the 'standard workflow' optimized for sequencing transcripts centered around 2kb. Additionally one Library (input HNR_S2) was prepared according an optimized 'long workflow' to enrich for larger transcripts up to >10kb. To further enhance the capture of full-length transcripts for USH2A and ADGRV1 (USH2C) genes, we also employed a targeted enrichment approach using the Samplix Xdrop System, followed by PacBio long-read sequencing. USH2A and ADGRV1 enrichment was performed by targeting '5- mid and 3' targets of the respective genes. Finally, we also added ONT (Oxford Nanopore technology) long-read mRNA sequencing of three independent neural retina samples. These data were used for the validation of events observed from the Iso-Seq and Samplix data. The ONT datasets contain sequencing data of the Usher-associated genes. Files are raw BAM, and CRAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.	Sequel II unspecified	8

Publications	Citations
A proteogenomic atlas of the human neural retina. Riepe TV, Stemerdink M, Salz R, Rey AD, de Bruijn SE, Boonen E, Tomkiewicz TZ, Kwint M, Gloerich J, Wessels HJCT, Delanote E, De Baere E, van Nieuwerburgh F, De Keulenaer S, Ferrari B, Ferrari S, Coppieters F, Cremers FPM, van Wyk E, Roosing S, de Vrieze E, 't Hoen PAC. Front Genet 15: 2024 1451024	0