HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 13 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
- 13 samples: 3 × CLIP_HMGN5 vs 2 × ChIP_HMGN5+ vs 2 × ChIP_HMGN5 vs 2 × CLIP_GFPGroups 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.
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 GSE166103_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 PRJNA699264 and SRA study SRP304545. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 2 as controls.
How we read this: 4 replicated groups read from 13 sample titles; they account for 9 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.
- GSM5061706 OverExpression
- GSM5061707 Control
- GSM5061708 knockdown
- GSM5061776 ChIP_GFP+ control
- GSM5061777 ChIP_HMGN5+R1 ChIP_HMGN5+
- GSM5061778 ChIP_HMGN5+R2 ChIP_HMGN5+
- GSM5061779 ChIP_HMGN5-R1 ChIP_HMGN5
- GSM5061780 ChIP_HMGN5-R2 ChIP_HMGN5
- GSM5061799 CLIP_GFP_R1 CLIP_GFP
- GSM5061800 CLIP_GFP_R2 CLIP_GFP
- GSM5061801 CLIP_HMGN5_R1 CLIP_HMGN5
- GSM5061802 CLIP_HMGN5_R2 CLIP_HMGN5
- GSM5061803 CLIP_HMGN5_R3 CLIP_HMGN5
- GSE254732 Inhibition of PCSK9 with evolocumab modulates lipoproteins and monocyte activation in high-risk ASCVD subjects 215 samples shares activation, protein
- GSE311573 Disordered protein LAT encodes relative levels of signaling pathways in T cell activation 62 samples shares activation, protein
- GSE282668 TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration 54 samples shares activation, protein
- GSE311572 Disordered protein LAT encodes relative levels of signaling pathways in T cell activation [Perturb-CITE-seq] 22 samples shares activation, protein
- GSE311565 Disordered protein LAT encodes relative levels of signaling pathways in T cell activation [Perturb-ATAC-seq] 18 samples shares activation, protein
- GSE274283 Bulk RNA sequencing analysis of a iPSC-derived neurons, microglia and astrocytes models of mitochondrial unfolded protein response (UPRmt) activation. 18 samples shares activation, protein
- GSE289881 Exploring fibroblast activation protein as an early biomarker in chronic lung allograft dysfunction 10 samples shares activation, protein
- GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares activation, chromatin
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.