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A foundational atlas of autism protein interactions reveals molecular convergence [CUT&Tag]

GSE285273 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2024/12/25 Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
16 samples: 8 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
A foundational atlas of autism protein interactions reveals molecular convergencebioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification.
Read the full summary ↓
A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
Published in
A foundational atlas of autism protein interactions reveals molecular convergence
Wang B, Vartak R, Zaltsman Y et al. · bioRxiv : the preprint server for biology 2024 · PMID 38076945 · doi:10.1101/2023.12.03.569805
This dataset
Open GSE285273 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE285273_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1202141 and SRA study SRP553421. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38076945) ↗
Study design
8 conditions, mostly in duplicate
WT forebrain organoids, CUTTag for FOXP1, lib… ×2 WT forebrain organoids, CUTTag for FOXP4, lib… ×2 WT forebrain organoids, CUTTag for H3K27me3, … ×2 WT forebrain organoids, CUTTag IgG negative c… ×2 R513H/WT forebrain organoids, CUTTag for FOXP… ×2 R513H/WT forebrain organoids, CUTTag for FOXP… ×2 R513H/WT forebrain organoids, CUTTag for H3K2… ×2 R513H/WT forebrain organoids, CUTTag IgG nega… ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
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