RNA sequencing data from the CLL cell line HG3 (HG-3) by Oxford Nanopore Technologies based direct RNA long-read sequencing.

This is the sequencing data from direct RNA long-read sequencing by Oxford Nanopore Technologies of the chronic lymphocytic leukemia cell line HG3 (HG-3).

Total RNA was extracted using the RNAeasy kit (Qiagen, Hilden, Germany). Sequencing libraries were generated from ~5 ?g of high-quality RNA (RIN >9.7) as assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). The direct RNA Sequencing kit (SQK- RNA002; Oxford Nanopore Technologies, Oxford, UK) was used according to the manufacturerÕs recommendations. Sequencing libraries were sequenced on a PromethION (Oxford Nanopore Technologies, Oxford, UK) using PromethION R9.4.1 flow cells (Oxford Nanopore Technologies, Oxford, UK). Basecalling was performed using Guppy v6.1.2 and passed FASTQ files were analyzed using nf-core/nanoseq v1.1.0 pipeline1. The FASTQ files were aligned to the reference genome hg19 using Minimap2 v2.1717. The resulting bam and index file are deposited here.

The data has been used in the publication by Hagerstrand and Oder et al. The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia, Leukemia 2024 (https://doi.org/10.1038/s41375-024-02379-4).

Researchers are welcome to use the data contained in the dataset for any scientific projects according to license CC BY-NC-ND 4.0.