RNA sequencing KdVS-drug screen 2025

Verboven, A.
Puvogel , S.
Latour, B.
Kolsters, N.
Lewerissa, E.I.
Mijdam, R.
Dyke, E.
Duineveld, D.
Zoodsma, M.
Claassen, W.
Oudakker, A.
Schoenmaker, C.
Koolen, D.
de Vries, B.
Linda, K.
't Hoen, P.A.C.
Nadif Kasri, N.

This repository contains RNA sequencing data, including raw FASTQ files and a processed count table, from human pluripotent stem cell–derived neurons co-cultured with wild-type rat astrocytes. Samples include two control lines (C1 and C4) and three lines with KANSL1 haploinsufficiency associated with Koolen-de Vries Syndrome (KdVS; KdVS1, KdVS2, KdVS3). RNA sequencing was performed for DMSO-treated controls (C1 and C4) and for DMSO-, phloretin-, and fasudil (1 µM)-treated KdVS neurons at 30 days in vitro (DIV30), following treatment initiation at DIV16. Four technical replicates were included per condition. Total RNA was isolated using the Zymo Quick-RNA Microprep Kit, and RNA integrity was confirmed with Agilent High Sensitivity Tapestation (RIN 9.9–10). cDNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit and sequenced (paired-end) on an Illumina NovaSeq X platform at the Utrecht Sequencing Facility (USEQ), The Netherlands. Read preprocessing was performed with fastp to trim adapters and remove PolyG artifacts. Seal (BBTools) was used to separate rat and human reads by mapping to Rnor_6.0 and GRCh38 reference genomes, with “ambig=first” used to assign ambiguous reads. Human reads were aligned to GRCh38 using HISAT2 with --rna-strandness FR, followed by sorting and indexing with SAMtools. UMI-tools was used for deduplication, and gene-level quantification was performed with Subread’s featureCounts. The repository includes paired-end FASTQ files (human reads only; R1 and R2 per sample), the all_featurecounts.txt file containing the processed count matrix, and a Metadata.xlsx file providing detailed information for each file in the repository. The Metadata includes attributes such as library strategy, organism, tissue, cell line, cell type, genotype, treatment, time point, molecule type, single or paired-end status, instrument model, processed data file, and raw file identifiers, formatted according to standard public RNA-seq data submission guidelines.