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TranscriptomicsCapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing
Here we describe CapTrap-Seq, an experimental workflow designed to address the problem of reduced transcript end detection by long-read RNA sequencing methods, especially at the 5' ends. We apply CapTrap-Seq to profile transcriptomes of the human heart and brain and we compared the obtained results ...
ORGANISM(S): Mus musculus 
2023-12-20 | E-MTAB-13063 | biostudies-arrayexpress
TranscriptomicsSingle cell short- and long-read RNA-sequencing of iNeurons in Fragile-X and control cell-lines
This study benchmarks bulk and single-cell long-read RNA sequencing technologies in a human neuronal model of Fragile X syndrome. NGN2-induced neurons were generated from patient-derived iPSCs carrying a silenced FMR1 gene (FXS line E3) and an isogenic CRISPR-corrected rescue line (IsoB11) in which ...
ORGANISM(S): Homo sapiens 
2025-03-30 | E-MTAB-16805 | biostudies-arrayexpress
ProteomicsLong read proteogenomics to characterize protein isoform diversity in human umbilical vein endothelial cells (HUVECs)
Mass spectrometry-based proteomics sample preparation Harvested HUVECs, approximately 5 million cells each, were pelleted and frozen at -80C. The sample pellet was lysed according to the Filter Aided Sample Preparation (FASP) protocol.59 Lysis buffer used in the FASP was changed to 6% SDS, 150 mM DT...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-04-28 | MSV000089326 | MassIVE
GenomicsPacbio Hifi sequencing of a naked mole-rat male subordinate kidney sample
Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) an...
ORGANISM(S): Heterocephalus glaber 
2026-08-05 | E-MTAB-17313 | biostudies-arrayexpress
TranscriptomicsBulk short- and long-read RNA-sequencing of iNeurons in Fragile-X and control cell-lines
This study benchmarks bulk and single-cell long-read RNA sequencing technologies in a human neuronal model of Fragile X syndrome. NGN2-induced neurons were generated from patient-derived iPSCs carrying a silenced FMR1 gene (FXS line E3) and an isogenic CRISPR-corrected rescue line (IsoB11) in which ...
ORGANISM(S): Homo sapiens 
2026-03-25 | E-MTAB-16791 | biostudies-arrayexpress
ProteomicsA proteogenomic atlas of the human neural retina
The human neural retina is enriched for alternative splicing, and it is estimated that more than 10% of variants associated with inherited retinal diseases (IRDs) alter splicing. Previous research mainly used short-read RNA-sequencing techniques to investigate retina-specific splicing and splicing f...
ORGANISM(S): Homo sapiens (Human) 
2024-10-17 | PXD045187 | Pride
Human Pacbio long-read rna-sequencing Proteogenomics Neural retina Msfragger Dda-pasef 
ProteomicsLong-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
Deregulated gene expression is a hallmark of cancer, however most studies to date have analyzed short-read RNA-sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short read RNA sequencing to comprehensively survey the tra...
ORGANISM(S): Homo sapiens (Human) 
2021-02-02 | PXD023373 | Pride
Isoform sequencing (iso-seq) Alternative promoters Gastric cancer Long-read sequencing 
TranscriptomicsLong-read ONT-dRNA and PacBio Kinnex full-length RNA sequencing of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system
UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation...
ORGANISM(S): Homo sapiens 
2025-06-01 | E-MTAB-14725 | biostudies-arrayexpress
UnknownA Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification.
Not available
S-EPMC12157514 | biostudies-literature
GenomicsPacbio Hifi sequencing of a male cape dune mole-rat kidney sample
One PacBio Hifi sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample ...
ORGANISM(S): Bathyergus suillus 
2026-08-05 | E-MTAB-17312 | biostudies-arrayexpress
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