Need Help?

Data access committee for neural retina and retinal organoid data

Contact Information

Dr Susanne Roosing
susanne.roosing@radboudumc.nl

Request Access

This DAC controls 3 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000100	Long-read (PacBio) sequencing of two retinal organoid samples. One sample was treated with cyclohexamide. Files are ccs BAM format files generated by a Sequel IIe machine.	Sequel IIe	2
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