Bouwen et al Nat Comm 2025 scRNAseq

The file contains single cell sequencing data of cortical neurons from 12 patient samples. 6 seizure and 6 non seizure patients.

I7_1382_01 Non seizure
- I17-1382-01-H072_cells_S24_L001_R1_001.fastq.gz
- I17-1382-01-H072_cells_S24_L002_R1_001.fastq.gz

I7_1425_01 Non seizure
- I17-1425-01-H078_PCs_S6_L001_R1_001.fastq.gz
- I17-1425-01-H078_PCs_S6_L002_R1_001.fastq.gz

I8_1031_01 Non seizure
- I18-1031-01-H085_PCs_S49_L001_R1_001.fastq.gz
- I18-1031-01-H085_PCs_S49_L002_R1_001.fastq.gz

I8_1105_01 Seizure
- I18-1105-01-H089_PCs_S40_L001_R1_001.fastq.gz
- I18-1105-01-H089_PCs_S40_L002_R1_001.fastq.gz

I8_1191-01 Non seizure
- I18-1190-01-H088_PCs_S38_L001_R1_001.fastq.gz
- I18-1190-01-H088_PCs_S38_L002_R1_001.fastq.gz

I8_1192_01 Seizure
- I18-1192-01-H093_PC_S18_L001_R1_001.fastq.gz
- I18-1192-01-H093_PC_S18_L002_R1_001.fastq.gz

I8_1201_01 Seizure
- I18-1201-01-H094_PC_S4_L001_R1_001.fastq.gz
- I18-1201-01-H094_PC_S4_L002_R1_001.fastq.gz

I8_1425_01 Non seizure
- I18-1425-01_S25_L001_R1_001.fastq.gz
- I18-1425-01_S25_L002_R1_001.fastq.gz

I8_1430_01Non seizure
- I18-1430-01_S26_L001_R1_001.fastq.gz
- I18-1430-01_S26_L002_R1_001.fastq.gz

I8_1455_01 Seizure
- I18-1455-01_S3_L001_R1_001.fastq.gz
- I18-1455-01_S3_L002_R1_001.fastq.gz

I9_1026_01Non seizure
- I19-1026-01_S11_L001_R1_001.fastq.gz
- I19-1026-01_S11_L002_R1_001.fastq.gz

I9_1035_01 Seizure
- I19-1035-01_S34_L001_R1_001.fastq.gz
- I19-1035-01_S34_L002_R1_001.fastq.gz

Patch-seq using Smart-seq2 protocol for human neurons
In a sub set of patient samples we harvested pyramidal cells for modified patchSeq analysis using the protocol for Smart-seq2. From sliced cortical samples, cell contents were harvested and processed according to the methods as described. Next, single-cell mRNA was converted to cDNA and sequencing libraries were created. DNA libraries for sequencing were prepared from cDNA libraries with the Illumina Nextera XT kit. The libraries were sequenced on an Illumina HiSeq2500 sequencer. Reads were generated of 50 base-pairs in length. Sequence adapters and poly-A were removed from the reads prior to alignment.