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High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing

GSE250435 Homo sapiens (human) RNA-seq (gene expression) 23 samples Submitted 2024/05/20 Platform GPL26167Platform GPL24106Platform GPL26180Platform GPL28352Platform GPL16791Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 23 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
23 samples: 9 conditions, mostly in duplicateGroups 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
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicingNucleic acids research · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing
Shekhar R, O'Grady T, Keil N et al. · Nucleic acids research 2024 · PMID 38922687 · doi:10.1093/nar/gkae540
This dataset
Open GSE250435 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE250435_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1054059 and SRA study SRP478604. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38922687) ↗
Study design
9 conditions, mostly in duplicate
Uninduced BCBL ×2 24h Induced BCBL ×2 48h Induced BCBL ×2 48 h Induced BCBL-1 B ×2 KSHV-Enriched 48 h Induced BCBL-1 B ×2 BCBL-1_48h_induced_B ×2 KSHV_Enriched_BCBL-1_48h_induced_B ×2 KSHV_Enriched_BCBL-1_48h_induced_1.5-3Kb_B ×2 +6 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 23 sample titles; they account for 18 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.

Samples in this study
Datasets on a similar topic

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