Variant-specific disruption to Notch signaling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic vesicles [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 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
- 11 samples: 5 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
- Variant-specific disruption to notch signalling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic cup-like organoidsBiochimica et biophysica acta. Molecular basis of disease · 2025
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 GSE288050_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 PRJNA1215938 and SRA study SRP559973. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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.
- GSM8758025 AN Clone 1, day 35, replicate 2
- GSM8758026 AN Clone 2, day 35, replicate 1 AN Clone 2, day 35,
- GSM8758027 AN Clone 2, day 35, replicate 2 AN Clone 2, day 35,
- GSM8758028 PX Clone 1, day 35, rep[licate 1 PX Clone 1, day 35, rep…
- GSM8758029 PX Clone 1, day 35, rep[licate 2 PX Clone 1, day 35, rep…
- GSM8758030 PX Clone 2, day 35, rep[licate 1 PX Clone 2, day 35, rep…
- GSM8758031 PX Clone 2, day 35, rep[licate 2 PX Clone 2, day 35, rep…
- GSM8758032 WT Clone 1, day 35, replicate 1 WT Clone 1, day 35,
- GSM8758033 WT Clone 1, day 35, replicate 2 WT Clone 1, day 35,
- GSM8758034 WT Clone 2, day 35, replicate 1 WT Clone 2, day 35,
- GSM8758035 WT Clone 2, day 35, replicate 2 WT Clone 2, day 35,
- GSE288049 Variant-specific disruption to Notch signaling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic vesicles 70 samples shares pax6, variant-specific, patient-derived, microphthalmia, disruption, aniridia, vesicles
- GSE291907 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [ATAC-seq] 10 samples shares pax6, atac-seq
- GSE298042 ATAC-Seq of Patient-Derived Xenografts in Metastatic Castration Resistant Prostate Cancer (LuCaP Series) 77 samples shares patient-derived, atac-seq
- GSE246044 Chromatin accessibility and transcriptomic responses to HDAC inhibitors in TP53 mutated patient-derived colon cancer organoids [ATAC-seq] 12 samples shares patient-derived, atac-seq
- GSE265940 Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models 48 samples shares patient-derived, microphthalmia
- GSE307222 Patient-derived cornea organoids as drug repurposing models for aniridia-associated keratopathy 9 samples shares patient-derived, aniridia
- GSE291908 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation 20 samples shares pax6
- GSE291903 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [RNA-seq 1] 14 samples shares pax6
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.