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Ancestralization of the modern human aryl hydrocarbon receptor by genome editing

GSE210514 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2024/06/26 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 60 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
60 samples: 10 conditions, mostly with about 6 replicates eachGroups 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
The modern human aryl hydrocarbon receptor is more active when ancestralized by genome editingProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
The aryl hydrocarbon receptor (AHR) is a transcription factor that upon binding ligands induces the expression of cytochrome P450 genes, which encode enzymes that metabolize aromatic hydrocarbons. The AHR carries an amino acid substitution at position 381 in all present-day humans that occurred after the divergence of modern humans from Neandertals and Denisovans. Here, we use genome editing to revert position 381 back to the ancestral state in human cells. Cells were treated with ligands for 4 h followed by RNA extraction and RNA-Seq.
Published in
The modern human aryl hydrocarbon receptor is more active when ancestralized by genome editing
Helmbrecht N, Lackner M, Maricic T et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 38739836 · doi:10.1073/pnas.2402159121
This dataset
Open GSE210514 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 GSE210514_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 PRJNA865939 and SRA study SRP389899. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38739836) ↗
Study design
10 conditions, mostly with about 6 replicates each
Ancestralized AHR, 50 nM benzo(a)pyrene, 4h, … ×6 Ancestralized AHR, 5 µM CH-223191, 4h, biol ×6 Ancestralized AHR, 0.05% DMSO, 4h, biol ×6 Ancestralized AHR, 10 nM indirubin, 4h, biol ×6 Ancestralized AHR, 100 nM kynurenic acid, 4h,… ×6 Modern human AHR, 50 nM benzo(a)pyrene, 4h, b… ×6 Modern human AHR, 5 µM CH-223191, 4h, biol ×6 Modern human AHR, 0.05% DMSO, 4h, biol ×6 +2 more

Supports a between-group comparison across 60 samples.

How we read this: 10 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

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.