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Data files used in the Pheniqs SPLiTSeq protocol

FASTQ file from SRA

Project: PRJNA434658

To facilitate scalable profiling of single cells, we developed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path towards comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems. Overall design: Single-cell/nucleus RNA-seq was performed using SPLiT-seq This code explains how to read the data from the paper into python: https://gist.github.com/Alex-Rosenberg/5ee8b14ea580144facad9c2b87cebf10

Project metadata in JSON

Raw FASTQ files downloaded from EBI ftp site.

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/001/SRR6750041/SRR6750041_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/001/SRR6750041/SRR6750041_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/002/SRR6750042/SRR6750042_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/002/SRR6750042/SRR6750042_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/003/SRR6750043/SRR6750043_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/003/SRR6750043/SRR6750043_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/004/SRR6750044/SRR6750044_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/004/SRR6750044/SRR6750044_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/005/SRR6750045/SRR6750045_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/005/SRR6750045/SRR6750045_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/006/SRR6750046/SRR6750046_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/006/SRR6750046/SRR6750046_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/007/SRR6750047/SRR6750047_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/007/SRR6750047/SRR6750047_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/008/SRR6750048/SRR6750048_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/008/SRR6750048/SRR6750048_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/009/SRR6750049/SRR6750049_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/009/SRR6750049/SRR6750049_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/000/SRR6750050/SRR6750050_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/000/SRR6750050/SRR6750050_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/001/SRR6750051/SRR6750051_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/001/SRR6750051/SRR6750051_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/002/SRR6750052/SRR6750052_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/002/SRR6750052/SRR6750052_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/003/SRR6750053/SRR6750053_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/003/SRR6750053/SRR6750053_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/004/SRR6750054/SRR6750054_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/004/SRR6750054/SRR6750054_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/005/SRR6750055/SRR6750055_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/005/SRR6750055/SRR6750055_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/006/SRR6750056/SRR6750056_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/006/SRR6750056/SRR6750056_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/007/SRR6750057/SRR6750057_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/007/SRR6750057/SRR6750057_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/008/SRR6750058/SRR6750058_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/008/SRR6750058/SRR6750058_2.fastq.gz

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/009/SRR6750059/SRR6750059_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR675/009/SRR6750059/SRR6750059_2.fastq.gz

Experiment SRX3722697 Data: SRR6750041 Description: NextSeq 550 paired end sequencing; GSM3017260: 100_CNS_nuclei; Mus musculus; RNA-Seq

Experiment SRX3722698 Data: SRR6750042, SRR6750043, SRR6750044, SRR6750045, SRR6750046, SRR6750047, SRR6750048, SRR6750049, SRR6750050, SRR6750051, SRR6750052, SRR6750053, SRR6750054, SRR6750055 Description: NextSeq 550 paired end sequencing; GSM3017261: 150000_CNS_nuclei; Mus musculus; RNA-Seq

Experiment SRX3722699 Data: SRR6750056 Description: NextSeq 550 paired end sequencing; GSM3017262: same_day_cells_nuclei_3000_UBCs; Homo sapiens; Mus musculus; RNA-Seq

Experiment SRX3722700 Data: SRR6750057 Description: NextSeq 550 paired end sequencing; GSM3017263: same_day_cells_nuclei_300_UBCs; Homo sapiens; Mus musculus; RNA-Seq

Experiment: SRX3722701 Data: SRR6750058 Description: NextSeq 550 paired end sequencing; GSM3017264: frozen_preserved_cells_nuclei_1000_UBCs; Homo sapiens; Mus musculus; RNA-Seq

Experiment SRX3722702 Data: SRR6750059 Description: NextSeq 550 paired end sequencing; GSM3017265: frozen_preserved_cells_nuclei_200_UBCs; Homo sapiens; Mus musculus; RNA-Seq