HMGN3 ChIP-seq in AC16 cells and Bulk-RNAseq in AC16 cell with and without HMGN3 knockdown
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 samples: 3 × AC16 cell, wildtype, BulkRNA-seq, vs 3 × AC16 cell, HMGN3 knockdown, BulkRNA-seq, vs 3 × AC16 cell, wildtype, ChIP-seq, vs 3 × AC16 cell, HMGN3 knockdown, ChIP-seq,Groups 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
- Chromatin structural gene expression stratifies cardiac cell populations in health and diseaseEpigenetics · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE306626_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1311517 and SRA study SRP613704. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 6 as controls.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9204851 AC16 cell, wildtype, BulkRNA-seq, replicate 1 AC16 cell, wildtype, Bu…
- GSM9204852 AC16 cell, wildtype, BulkRNA-seq, replicate 2 AC16 cell, wildtype, Bu…
- GSM9204853 AC16 cell, wildtype, BulkRNA-seq, replicate 3 AC16 cell, wildtype, Bu…
- GSM9204854 AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 1 AC16 cell, HMGN3 knockd…
- GSM9204855 AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 2 AC16 cell, HMGN3 knockd…
- GSM9204856 AC16 cell, HMGN3 knockdown, BulkRNA-seq, replicate 3 AC16 cell, HMGN3 knockd…
- GSM9204857 AC16 cell, wildtype, ChIP-seq, replicate 1 AC16 cell, wildtype, Ch…
- GSM9204858 AC16 cell, wildtype, ChIP-seq, replicate 2 AC16 cell, wildtype, Ch…
- GSM9204859 AC16 cell, wildtype, ChIP-seq, replicate 3 AC16 cell, wildtype, Ch…
- GSM9204860 AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 1 AC16 cell, HMGN3 knockd…
- GSM9204861 AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 2 AC16 cell, HMGN3 knockd…
- GSM9204862 AC16 cell, HMGN3 knockdown, ChIP-seq, replicate 3 AC16 cell, HMGN3 knockd…
- GSE229482 ChIP-Seq analysis of H3K4me3 and H3K27ac histone marks without and with METTL8 knockdown 24 samples shares knockdown, chip-seq, without
- GSE277805 RNA-seq analysis using A549 cells with TRIM22 knockdown and control A549 cells with or without ionizing radiation treatment. 12 samples shares knockdown, without
- GSE216922 ChIP-Seq of MYC in MCF-7 cells with EPIC1 knockdown or overexpression. 10 samples shares knockdown, chip-seq
- GSE303619 mRNA sequencing of human AC16 cells expressing PCBP1, PCBP2, or both 12 samples shares ac16
- GSE261096 Molecular mechanism of EP300 in AC16 cell line 12 samples shares ac16
- GSE302553 Pathogenetic mechanisms of muscle-specific ribosomes in dilated cardiomyopathy (AC16 RNA-seq) 42 samples shares ac16
- GSE338719 Transcriptomic changes in human AC16 cardiomyocytes induced by electronic cigarette aerosol exposure 20 samples shares ac16
- GSE338135 NRAS knockdown reverses monocytic cell state and resensitizes resistant FLT3-AML cells to gilteritinib 75 samples shares knockdown
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.