Long-read Transcripts CLS long-read RNAs Track Settings

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Capture long-seq long-read lncRNAs

Track collection: Transcripts and other data generated using long-read sequencing technology (PacBio and Oxford Nanopore)

Description

All tracks in this collection (2)

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Label: Target number

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Select subtracks by type and sample:

All	*Type*	Targets	Models	Pre-capture ONT models	Pre-capture PacBio models	Post-capture ONT models	Post-capture PacBio models	Pre-capture ONT reads	Pre-capture PacBio reads	Post-capture ONT reads	Post-capture PacBio reads	*Type*	All
*Sample*												*Sample*
Combined												Combined
Adult Brain												Adult Brain
Embryonic Brain												Embryonic Brain
Cell Line Pool												Cell Line Pool
Adult Heart												Adult Heart
Embryonic Heart												Embryonic Heart
Adult Liver												Adult Liver
Embryonic Liver												Embryonic Liver
Placenta												Placenta
Adult Testis												Adult Testis
Tissue Pool												Tissue Pool
Adult Blood												Adult Blood
Embryonic iPSC												Embryonic iPSC

List subtracks: only selected/visible all ()
	dense	CLS targets	CLS target regions	Schema
	pack	CLS transcripts	CLS transcript models	Schema
	squish Configure	Blood models	Adult Blood transcript models	Schema
	dense Configure	Blood ONT post models	Adult Blood ONT post-capture transcript models	Schema
	squish Configure	Blood ONT post reads	Adult Blood ONT post-capture reads	Schema
	dense Configure	Blood ONT pre models	Adult Blood ONT pre-capture transcript models	Schema
	squish Configure	Blood ONT pre reads	Adult Blood ONT pre-capture reads	Schema
	dense Configure	Blood PB post models	Adult Blood PacBio post-capture transcript models	Schema
	squish Configure	Blood PB post reads	Adult Blood PacBio post-capture reads	Schema
	dense Configure	Blood PB pre models	Adult Blood PacBio pre-capture transcript models	Schema
	squish Configure	Blood PB pre reads	Adult Blood PacBio pre-capture reads	Schema
	squish Configure	Brain models	Adult Brain transcript models	Schema
	dense Configure	Brain ONT post models	Adult Brain ONT post-capture transcript models	Schema
	squish Configure	Brain ONT post reads	Adult Brain ONT post-capture reads	Schema
	dense Configure	Brain ONT pre models	Adult Brain ONT pre-capture transcript models	Schema
	squish Configure	Brain ONT pre reads	Adult Brain ONT pre-capture reads	Schema
	dense Configure	Brain PB post models	Adult Brain PacBio post-capture transcript models	Schema
	squish Configure	Brain PB post reads	Adult Brain PacBio post-capture reads	Schema
	dense Configure	Brain PB pre models	Adult Brain PacBio pre-capture transcript models	Schema
	squish Configure	Brain PB pre reads	Adult Brain PacBio pre-capture reads	Schema
	squish Configure	Cell Line Pool models	Cell Line Pool transcript models	Schema
	dense Configure	Cell Line Pool ONT post models	Cell Line Pool ONT post-capture transcript models	Schema
	squish Configure	Cell Line Pool ONT post reads	Cell Line Pool ONT post-capture reads	Schema
	dense Configure	Cell Line Pool ONT pre models	Cell Line Pool ONT pre-capture transcript models	Schema
	squish Configure	Cell Line Pool ONT pre reads	Cell Line Pool ONT pre-capture reads	Schema
	dense Configure	Cell Line Pool PB post models	Cell Line Pool PacBio post-capture transcript models	Schema
	squish Configure	Cell Line Pool PB post reads	Cell Line Pool PacBio post-capture reads	Schema
	dense Configure	Cell Line Pool PB pre models	Cell Line Pool PacBio pre-capture transcript models	Schema
	squish Configure	Cell Line Pool PB pre reads	Cell Line Pool PacBio pre-capture reads	Schema
	squish Configure	Emb Brain models	Embryonic Brain transcript models	Schema
	dense Configure	Emb Brain ONT post models	Embryonic Brain ONT post-capture transcript models	Schema
	squish Configure	Emb Brain ONT post reads	Embryonic Brain ONT post-capture reads	Schema
	dense Configure	Emb Brain ONT pre models	Embryonic Brain ONT pre-capture transcript models	Schema
	squish Configure	Emb Brain ONT pre reads	Embryonic Brain ONT pre-capture reads	Schema
	dense Configure	Emb Brain PB post models	Embryonic Brain PacBio post-capture transcript models	Schema
	squish Configure	Emb Brain PB post reads	Embryonic Brain PacBio post-capture reads	Schema
	dense Configure	Emb Brain PB pre models	Embryonic Brain PacBio pre-capture transcript models	Schema
	squish Configure	Emb Brain PB pre reads	Embryonic Brain PacBio pre-capture reads	Schema
	squish Configure	Emb Heart models	Embryonic Heart transcript models	Schema
	dense Configure	Emb Heart ONT post models	Embryonic Heart ONT post-capture transcript models	Schema
	squish Configure	Emb Heart ONT post reads	Embryonic Heart ONT post-capture reads	Schema
	dense Configure	Emb Heart ONT pre models	Embryonic Heart ONT pre-capture transcript models	Schema
	squish Configure	Emb Heart ONT pre reads	Embryonic Heart ONT pre-capture reads	Schema
	dense Configure	Emb Heart PB post models	Embryonic Heart PacBio post-capture transcript models	Schema
	squish Configure	Emb Heart PB post reads	Embryonic Heart PacBio post-capture reads	Schema
	dense Configure	Emb Heart PB pre models	Embryonic Heart PacBio pre-capture transcript models	Schema
	squish Configure	Emb Heart PB pre reads	Embryonic Heart PacBio pre-capture reads	Schema
	squish Configure	Emb iPSC models	Embryonic iPSC transcript models	Schema
	dense Configure	Emb iPSC ONT post models	Embryonic iPSC ONT post-capture transcript models	Schema
	squish Configure	Emb iPSC ONT post reads	Embryonic iPSC ONT post-capture reads	Schema
	dense Configure	Emb iPSC ONT pre models	Embryonic iPSC ONT pre-capture transcript models	Schema
	squish Configure	Emb iPSC ONT pre reads	Embryonic iPSC ONT pre-capture reads	Schema
	dense Configure	Emb iPSC PB post models	Embryonic iPSC PacBio post-capture transcript models	Schema
	squish Configure	Emb iPSC PB post reads	Embryonic iPSC PacBio post-capture reads	Schema
	dense Configure	Emb iPSC PB pre models	Embryonic iPSC PacBio pre-capture transcript models	Schema
	squish Configure	Emb iPSC PB pre reads	Embryonic iPSC PacBio pre-capture reads	Schema
	squish Configure	Emb Liver models	Embryonic Liver transcript models	Schema
	dense Configure	Emb Liver ONT post models	Embryonic Liver ONT post-capture transcript models	Schema
	squish Configure	Emb Liver ONT post reads	Embryonic Liver ONT post-capture reads	Schema
	dense Configure	Emb Liver ONT pre models	Embryonic Liver ONT pre-capture transcript models	Schema
	squish Configure	Emb Liver ONT pre reads	Embryonic Liver ONT pre-capture reads	Schema
	dense Configure	Emb Liver PB post models	Embryonic Liver PacBio post-capture transcript models	Schema
	squish Configure	Emb Liver PB post reads	Embryonic Liver PacBio post-capture reads	Schema
	dense Configure	Emb Liver PB pre models	Embryonic Liver PacBio pre-capture transcript models	Schema
	squish Configure	Emb Liver PB pre reads	Embryonic Liver PacBio pre-capture reads	Schema
	squish Configure	Heart models	Adult Heart transcript models	Schema
	dense Configure	Heart ONT post models	Adult Heart ONT post-capture transcript models	Schema
	squish Configure	Heart ONT post reads	Adult Heart ONT post-capture reads	Schema
	dense Configure	Heart ONT pre models	Adult Heart ONT pre-capture transcript models	Schema
	squish Configure	Heart ONT pre reads	Adult Heart ONT pre-capture reads	Schema
	dense Configure	Heart PB post models	Adult Heart PacBio post-capture transcript models	Schema
	squish Configure	Heart PB post reads	Adult Heart PacBio post-capture reads	Schema
	dense Configure	Heart PB pre models	Adult Heart PacBio pre-capture transcript models	Schema
	squish Configure	Heart PB pre reads	Adult Heart PacBio pre-capture reads	Schema
	squish Configure	Liver models	Adult Liver transcript models	Schema
	dense Configure	Liver ONT post models	Adult Liver ONT post-capture transcript models	Schema
	squish Configure	Liver ONT post reads	Adult Liver ONT post-capture reads	Schema
	dense Configure	Liver ONT pre models	Adult Liver ONT pre-capture transcript models	Schema
	squish Configure	Liver ONT pre reads	Adult Liver ONT pre-capture reads	Schema
	dense Configure	Liver PB post models	Adult Liver PacBio post-capture transcript models	Schema
	squish Configure	Liver PB post reads	Adult Liver PacBio post-capture reads	Schema
	dense Configure	Liver PB pre models	Adult Liver PacBio pre-capture transcript models	Schema
	squish Configure	Liver PB pre reads	Adult Liver PacBio pre-capture reads	Schema
	squish Configure	Placenta models	Placenta transcript models	Schema
	dense Configure	Placenta ONT post models	Placenta ONT post-capture transcript models	Schema
	squish Configure	Placenta ONT post reads	Placenta ONT post-capture reads	Schema
	dense Configure	Placenta ONT pre models	Placenta ONT pre-capture transcript models	Schema
	squish Configure	Placenta ONT pre reads	Placenta ONT pre-capture reads	Schema
	dense Configure	Placenta PB post models	Placenta PacBio post-capture transcript models	Schema
	squish Configure	Placenta PB post reads	Placenta PacBio post-capture reads	Schema
	dense Configure	Placenta PB pre models	Placenta PacBio pre-capture transcript models	Schema
	squish Configure	Placenta PB pre reads	Placenta PacBio pre-capture reads	Schema
	squish Configure	Testis models	Adult Testis transcript models	Schema
	dense Configure	Testis ONT post models	Adult Testis ONT post-capture transcript models	Schema
	squish Configure	Testis ONT post reads	Adult Testis ONT post-capture reads	Schema
	dense Configure	Testis ONT pre models	Adult Testis ONT pre-capture transcript models	Schema
	squish Configure	Testis ONT pre reads	Adult Testis ONT pre-capture reads	Schema
	dense Configure	Testis PB post models	Adult Testis PacBio post-capture transcript models	Schema
	squish Configure	Testis PB post reads	Adult Testis PacBio post-capture reads	Schema
	dense Configure	Testis PB pre models	Adult Testis PacBio pre-capture transcript models	Schema
	squish Configure	Testis PB pre reads	Adult Testis PacBio pre-capture reads	Schema
	squish Configure	Tissue Pool models	Tissue Pool transcript models	Schema
	dense Configure	Tissue Pool ONT post models	Tissue Pool ONT post-capture transcript models	Schema
	squish Configure	Tissue Pool ONT post reads	Tissue Pool ONT post-capture reads	Schema
	dense Configure	Tissue Pool ONT pre models	Tissue Pool ONT pre-capture transcript models	Schema
	squish Configure	Tissue Pool ONT pre reads	Tissue Pool ONT pre-capture reads	Schema
	dense Configure	Tissue Pool PB post models	Tissue Pool PacBio post-capture transcript models	Schema
	squish Configure	Tissue Pool PB post reads	Tissue Pool PacBio post-capture reads	Schema
	dense Configure	Tissue Pool PB pre models	Tissue Pool PacBio pre-capture transcript models	Schema
	squish Configure	Tissue Pool PB pre reads	Tissue Pool PacBio pre-capture reads	Schema

Description

These tracks represent the results of targeted long-read RNA sequencing aimed at identifying lowly expressed lncRNAs in adult and embryonic tissues. The track consists of capture target regions, mappings of pre- and post-capture reads, and transcript models built from the data.

Portions of this dataset were used to develop the lncRNA annotations introduced in GENCODE v47. The data are a superset of the data incorporated into GENCODE. The transcript models for a given RNA do not necessarily match those in GENCODE and are provided as a guide to exploring the sequencing data.

Detailed descriptions of the data are available at the GENCODE CLS Project site.

Display Conventions and Configuration

This is a multi-view composite track containing multiple data types (views). Each view includes subtracks that are displayed individually in the browser. Instructions for configuring multi-view tracks are here.

Views:

Targets: Capture target regions
Models: Transcript models generated from reads and merging
Sample models: Transcript models by sample in which they were observed
Per-experiment reads: Read mappings per experiment
Per-experiment Models: Transcript models generated from the experiments

Methods

This project, led by the GENCODE consortium, employed the Capture Long-read Sequencing (CLS) protocol to enrich transcripts from targeted genomic regions. It used a large capture array with orthologous probes in human and mouse genomes, targeting non-GENCODE lncRNA annotations and regions suspected of unannotated transcription. CapTrap-Seq, a cDNA library preparation protocol, was used to enrich for full-length RNA molecules (5′ to 3′).

Matched adult and embryonic tissues from human and mouse were selected to maximize transcriptome complexity. Libraries were sequenced pre- and post-capture using PacBio and Oxford Nanopore Technologies (ONT) long-read platforms, as well as short-read technologies.

Transcript isoform models were built from reads using the LyRic analysis software. These were merged using intron chains, with transcription start and end sites anchored using CAGE and poly(A) data.

Credits

This dataset was developed by the Guigó Lab, Centre for Genomic Regulation (CRG) and the GENCODE consortium.
The track set was constructed by Sílvia Carbonell-Sala, Andrea Tanzer, and Mark Diekhans.

References

Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Mądry T, Jungreis I, Arnan C, Lagarde J, Borsari B et al. GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing. bioRxiv. 2024 Oct 31;. PMID: 39554180; PMC: PMC11565817

Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R et al. GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Res. 2025 Jan 6;53(D1):D966-D975. PMID: 39565199; PMC: PMC11701607

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods. 2024 Jul;21(7):1349-1363. PMID: 38849569; PMC: PMC11543605

Carbonell-Sala S, Perteghella T, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R. CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing. Nat Commun. 2024 Jun 27;15(1):5278. PMID: 38937428; PMC: PMC11211341

LyRic: Long RNA-seq analysis workflow https://github.com/guigolab/LyRic