Accurate isoform quantification by joint short- and long-read RNA-sequencing
RNA-seq (gene expression) · human · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 2 × Differentiated (day 41) - long reads vs 2 × Differentiated (day 61) - long reads vs 2 × Differentiated (day 41) - short reads vs 2 × Differentiated (day 61) - short readsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Accurate isoform quantification by joint short- and long-read RNA-sequencingbioRxiv : the preprint server for biology · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE271530_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1132164 and SRA study SRP518114. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 8 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8378893 hESC (day 0) – long reads - rep 1
- GSM8378894 hESC (day 0) - long reads - rep 2
- GSM8378895 Differentiated (day 41) - long reads - rep 1 Differentiated (day 41)…
- GSM8378896 Differentiated (day 41) - long reads - rep 2 Differentiated (day 41)…
- GSM8378897 Differentiated (day 61) - long reads - rep 1 Differentiated (day 61)…
- GSM8378898 Differentiated (day 61) - long reads - rep 2 Differentiated (day 61)…
- GSM8378899 hESC (day 0) – short reads - rep 1
- GSM8378900 hESC (day 0) - short reads - rep 2
- GSM8378901 Differentiated (day 41) - short reads - rep 1 Differentiated (day 41)…
- GSM8378902 Differentiated (day 41) - short reads - rep 2 Differentiated (day 41)…
- GSM8378903 Differentiated (day 61) - short reads - rep 1 Differentiated (day 61)…
- GSM8378904 Differentiated (day 61) - short reads - rep 2 Differentiated (day 61)…
- GSE282552 Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ] 18 samples shares long-read, isoform, short
- GSE303762 Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches 38 samples shares rna-sequencing, long-read
- GSE282551 Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [long-read RNAseq ] 30 samples shares long-read, isoform
- GSE224153 RNA-sequencing reveals strong predominance of THRA splicing isoform 2 in the developing and adult human brain 24 samples shares rna-sequencing, isoform
- GSE297994 Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms 22 samples shares long-read, isoform
- GSE315136 Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression 18 samples shares long-read, isoform
- GSE265988 Identification and quantification of gene isoforms during the differentiation of human embryonic stem cells into pharyngeal endoderm and primordial germ cell-like cells 18 samples shares quantification, isoform
- GSE250144 RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain 16 samples shares rna-sequencing, isoform
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.