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Iso Seq Public Datasets

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Elizabeth Tseng edited this page Oct 18, 2021 · 23 revisions

Last Updated: 2021/10/18

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)

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

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 S288C, CEN.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)

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