Iso Seq Public Datasets

Last Updated: 2022/02/11

• Human & Mouse - single-cell
• Human - whole transcriptome
• Human - targeted
• Plant & Animal
• Microbes & Viruses

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Human & Mouse - Single-Cell Iso-Seq

(1) Post-natal mouse brain

Key	Detail
Species	Mouse, postnatal brain
Sequencing	10X --> Sequel II
Analysis	Iso-Seq & R code
Data	GEO:GSE158450

Joglekar et al., "A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain", Nature Communications (2021)

(2) Mouse C2C12 cells (ENCODE project)

Key	Detail
Species	Mouse, C2C12 cells
Sequencing	Parse(SplitSeq) --> Sequel II
Analysis	Iso-Seq & R code
Data	GEO:GSE168776

Rebboah et al., "Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq", biorxiv (2021)

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Human - Whole Transcriptome

(1) HGSVC Human Transcriptome Samples (1000genomes)

Key	Detail
Species	12 HGSVC (Human Genome Structural Variation Consortium, Phase 2) samples; Human
Sequencing	Sequel II
Analysis	Iso-Seq
Data	1000GenomesFTP

(2) ENCODE Consortium, various cell lines

Key	Detail
Species	Human, various cell lines
Sequencing	Sequel I & II
Analysis	Iso-Seq + TALON
Data	ENCODE portal

Wyman et al., "A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification", bioRxiv (2019)

(3) Human fetal tissue; HAP1 cells, 2021

Key	Detail
Species	XpressRef Universal Total RNA (mixed adult and fetal tissues); HAP1 cells
Sequencing	Sequel II, RNA-Seq
Analysis	Iso-Seq
Data	GEO:GSE160383

Troskie et al., "Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome", Genome Biology (2021)

(4) Universal Human Reference RNA (UHRR), 2021 Release

Key	Detail
Species	Human, UHRR
Sequencing	Sequel II
Analysis	Iso-Seq
Data	UHRRisoseq2021
Browser	UCSC Genome Browser Track

This is PacBio's internal UHRR data release.

An associated publication that used the public UHRR dataset: Kuo et al., "Illuminating the dark side of the human transcriptome with long read transcript sequencing", BMC Genomics (2020)

(5) Alzheimer's Brain, 2020 Release

Key	Detail
Species	Human, Alzheimer whole brain
Sequencing	Sequel II
Analysis	Iso-Seq
Data	AlzIsoSeq
Browser	UCSC Genome Browser Track

This is PacBio's internal Alzheimer data release. PacBio blogpost here

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Plant & Animal

(1) Arabidopsis thaliana

Key	Detail
Species	A. thaliana, various tissues
Sequencing	Sequel I
Analysis	Iso-Seq & TAMA
Data	SRA PRJNA755474

Reference: Zhang et al. "A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis", biorxiv (2021)

(2) Atlantic salmon

Key	Detail
Species	Atlantic salmon (Salmo salar)
Sequencing	Sequel II
Analysis	Iso-Seq & SQANTI
Data	TSA:GIYK00000000

Ramberg et al., "A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon", Frontiers in Genetics (2021)

Microbes & Viruses

(1) Yeast

Key	Detail
Species	S. cerevisiae, S288C and CEN.PK
Sequencing	Sequel II
Analysis	Iso-Seq & custom code
Data	SRA PRJNA58809, genomeS288C, genomeCEN.PK

Fiddes et al., "Long read transcript sequencing of S. cerevisiae reveals complex transcriptional dynamics and improves analysis of scRNA-Seq", Biology of Genomes poster (2020)