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Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchE

GSE254457 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2025/11/13 Platform GPL30209
At a glance

RNA-seq (gene expression) · human · 30 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
30 samples: 10 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
KORE-Map 1.1: Korean medicine omics resource extension map on transcriptome data of dyspepsia herbal medicineBMC genomic data · 2026
Summary (written by the submitters)
This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in SW1783 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.
Published in
KORE-Map 1.1: Korean medicine omics resource extension map on transcriptome data of dyspepsia herbal medicine
Seo EH, Park M, Baek SJ et al. · BMC genomic data 2026 · PMID 41618141 · doi:10.1186/s12863-026-01409-7
This dataset
Open GSE254457 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 GSE254457_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 PRJNA1070608 and SRA study SRP486605. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41618141) ↗
Study design
10 conditions, mostly in triplicate
BatchE_Vehicle(DMSO)_second_sequencing ×3 BatchE_ethanol extract of Bojungikgi-tang (Hi… ×3 BatchE_ethanol extract of Bojungikgi-tang (Me… ×3 BatchE_ethanol extract of Bojungikgi-tang (Lo… ×3 BatchE_ethanol extract of Sayeok-tang (High d… ×3 BatchE_ethanol extract of Sayeok-tang (Medium… ×3 BatchE_ethanol extract of Sayeok-tang (Low do… ×3 BatchE_ethanol extract of Banhasasim-tang (Hi… ×2 +5 more

Supports a between-group comparison across 27 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 27 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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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.