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Gene syntax defines supercoiling-mediated transcriptional feedback [RNA-seq]

GSE316692 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/03/02 Platform GPL34295
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
Gene syntax defines supercoiling-mediated transcriptional feedbackScience (New York, N.Y.) · 2026
Summary (written by the submitters)
Gene syntax---the order and arrangement of genes and their regulatory elements---shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that the reciprocal effects of transcription and DNA supercoiling, which we term supercoiling-mediated feedback, regulates expression of adjacent genes in a syntax-specific manner.
Read the full summary ↓
Using a suite of chromatin state assays, we measure syntax- and induction-dependent formation of chromatin structures in human induced pluripotent stem cells. Applying syntax as a design parameter and without altering sequence or copy number, we built compact gene circuits, tuning the expression mean, noise, and stoichiometry across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.
Published in
Gene syntax defines supercoiling-mediated transcriptional feedback
Johnstone CP, Love KS, Kabaria SR et al. · Science (New York, N.Y.) 2026 · PMID 42060734 · doi:10.1126/science.adw1925
This dataset
Open GSE316692 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 GSE316692_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 PRJNA1403608 and SRA study SRP662978. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42060734) ↗
Study design
8 conditions, mostly in triplicate
Convergent hiPSC, induced, ×3 Convergent hiPSC, uninduced, ×3 Downstream tandem hiPSC, induced, ×3 Downstream tandem hiPSC, uninduced, ×3 Divergent hiPSC, induced, ×3 Divergent hiPSC, uninduced, ×3 Upstream tandem hiPSC, induced, ×3 Upstream tandem hiPSC, uninduced, ×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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