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Comparative analysis of gene expression in HepG2-NTCP_HA:HBc upon treatment with CAM-A or CAM-E

GSE263292 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/10/16 Platform GPL21290
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
CAM-A-dependent HBV core aggregation induces apoptosis through ANXA1JHEP reports : innovation in hepatology · 2024
Summary (written by the submitters)
HepG2-NTCP_HA:HBc cells stably express HBV core antigen. Treatment of these cells with CAM-A compounds (but not CAM-E) induces the abnormal nuclear aggregation of core leading to cell death via apoptosis in a time dependent manner. The goal of this project is to determine the transcriptomic modifications induced by CAM-A treatment in these cell lines at day 2 and day 3 post-treatment.
Published in
CAM-A-dependent HBV core aggregation induces apoptosis through ANXA1
Taverniti V, Meiss-Heydmann L, Gadenne C et al. · JHEP reports : innovation in hepatology 2024 · PMID 39386256 · doi:10.1016/j.jhepr.2024.101134
This dataset
Open GSE263292 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 GSE263292_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 PRJNA1096654 and SRA study SRP499948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39386256) ↗
Study design
8 conditions, mostly in triplicate
DMSO_day2 ×3 CAM-Ah_RG7907_day2 ×3 CAM-At_ALG5398_day2 ×3 CAM-E_ALG26_day2 ×3 DMSO_day3 ×3 CAM-Ah_RG7907_day3 ×3 CAM-At_ALG5398_day3 ×3 CAM-E_ALG26_day3 ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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