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18
datasets available to search
ShareScore release 0.9.0
Dataset results
18 results for “Long-read RNA-seq”
The PODER cross-ancestry long-read RNA-seq dataset
<p>Table legends:</p> <ul> <li>column_descriptions.docx: Extended description of columns in selected tables.</li> <li>00_sample_metadata: Sample and experimental metadata pertaining to each LR-RNA-seq sample.</li> <li>01_uma_gtf: Unfiltered merged annotation (UMA) GTF for all spliced intron chains discovered by each of the tools.</li> <li>02_uma_mt: Metadata table for SQANTI QC, Recount3 support, protein prediction, and other relevant characteristics for each transcript in the UMA annotation used to filter transcripts.</li> <li>03_poder_gtf: Final PODER GTF, including predicted CDSs for novel transcripts and annotated CDSs for known transcripts.</li> <li>04_poder_mt: Metadata table for SQANTI QC, Recount3 support, protein prediction, and other relevant characteristics for each transcript in PODER.</li> <li>06_poder_t_counts: PODER transcript counts in each sample as quantified by lr-kallisto.</li> <li>07_poder_g_counts: PODER gene counts in each sample as quantified by lr-kallisto.</li> <li>08_mage_t_counts_poder: Transcript counts for the MAGE RNA-seq dataset computed using the PODER annotation with kallisto.</li> <li>09_mage_t_counts_gencode: Transcript counts for the MAGE RNA-seq dataset computed using the GENCODE annotation with kallisto.</li> <li>10_mage_t_counts_enh: Transcript counts for the MAGE RNA-seq dataset computed using the Enhanced GENCODE annotation with kallisto.</li> <li>11_astu: Allele-specific transcript usage results.</li> <li>12_ase: Allele-specific expression results.</li> <li>13_mage_tau: Tau values for Enhanced GENCODE transcripts computed on the MAGE RNA-seq dataset.</li> <li>14_gwas_enrichments: GWAS enrichment results for ASTU genes overlapping GWAS genes.</li> <li>16_inter_catalog_overlap: Boolean detection of transcripts across PODER, annotations (GENCODE, RefSeq) and other RNA-seq / LR-RNA-seq-derived transcript catalogs (CHESS, GTEx, ENCODE4).</li> <li>17_personalized_hg38: Isoforms and their intron chains detected using personalized-GRCh38s.</li> <li>18_enh_gencode: Enhanced GENCODE GTF with novel transcripts from PODER added to all annotated transcripts from GENCODE v47</li> </ul>
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data (repository for simulated ONT RNA-seq data)
<p>Simulated ONT direct RNA and 1D cDNA sequencing data of varying sequencing depths (0.5 million, 1 million, 3 million, and 5 million simulated reads) used for benchmark evaluations of transcript discovery and quantification in our paper "ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data". All details can be found in the <strong>Materials and Methods</strong> section of the paper. </p> <p><em>HEK293T_DirectRNA.transcriptome_quantification.tsv</em> and <em>HEK293T_DirectRNA.transcriptome_quantification.tsv </em>are tab-separated files containing estimated raw read counts and normalized abundance values (in TPM) of transcripts annotated in GENCODE v34lift37. Transcript quantification was done using NanoSim (version 3.1.0). </p> <p><em>HEK293T_DirectRNA.NanoSim_500k.fastq.gz</em>,<em> </em><em>HEK293T_DirectRNA.NanoSim_1M.fastq.gz</em>, <em>HEK293T_DirectRNA.NanoSim_3M.fastq.gz</em>, and<em> HEK293T_DirectRNA.NanoSim_5M.fastq.gz </em>are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT direct RNA sequencing reads respectively. </p> <p><em>HEK293T_1DcDNA.NanoSim_500k.fastq.gz</em>,<em> HEK293T_1DcDNA.NanoSim_1M.fastq.gz</em>, <em>HEK293T_1DcDNA.NanoSim_3M.fastq.gz</em>, and<em> HEK293T_1DcDNA.NanoSim_5M.fastq.gz </em>are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT 1D cDNA sequencing reads respectively. </p>
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Open the record for dataset details and reuse information.
RNA-Seq analysis (long-reads) of human parental M238P and BRAF inhibitors-resistant M238R melanoma cells
GEO Series GSE171882. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data
GEO Series GSE192955. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
Reference Long-read Isoform-aware Transcriptomes of Activated Human CD4 T cells (PacBio Iso-Seq, matched to Illumina RNA-Seq Data)
GEO Series GSE229971. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Total RNA-seq and long-read RNAseq (Nanopore) upon Son KD in mouse embryonic stem cells
GEO Series GSE271659. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]
GEO Series GSE225377. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Set4: ERCC bulk Loop-seq long-read RNA-seq by Illumina NovaSeq platform
GEO Series GSE246835. synthetic construct. 2 samples. Type: Other.
Set3: ERCC bulk Loop-seq long-read RNA-seq by Element Biosciences AVITI platform
GEO Series GSE246834. synthetic construct. 2 samples. Type: Other.
Accurate long-read transcript discovery and quantification at single-cell resolution with Isosceles [RNA-seq]
GEO Series GSE248114. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
COVID-19 vaccination is associated with attenuation of inflammatory responses during breakthrough disease [long-read RNA-Seq]
GEO Series GSE228840. Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing.
Set5: HCC single-cell Loop-seq long-read RNA-seq by Element Biosciences AVITI platform
GEO Series GSE246836. Homo sapiens. 8 samples. Type: Other.
Long-read RNA-seq(Iso-seq) analysis of HBV-KMT2B integrated HPCs in which HBV genome is integrated into KMT2B region.
GEO Series GSE244522. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Identification of a novel transcriptional variant in the mouse Sry locus by long-read RNA-seq and conventional RNA-seq
GEO Series GSE151472. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
A long-read RNA-seq approach to identify novel transcripts of very large genes
GEO Series GSE138362. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Long-read RNA-Seq analysis of the full-length F8 transcript in iPSCs
GEO Series GSE229621. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
Reference Long-Read Transcriptomes of Human Peripheral Blood Lymphocytes (PacBio Iso-Seq, Matched to Illumina RNA-Seq Data)
GEO Series GSE202327. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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