Defining Cis-regulatory Elements and Transcription Factors that Control Human Cortical Interneuron Development
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 118 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
- 118 samples: 32 conditions, mostly with about 4 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
- Defining cis-regulatory elements and transcription factors that control human cortical interneuron developmentiScience · 2024
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 GSE239481_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 PRJNA999364 and SRA study SRP451778. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 118 samples.
How we read this: 32 replicated groups read from 118 sample titles; they account for 118 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.
- GSM7664083 H9 WT D0 RNAseq Replicate 1 H9 WT D0 RNAseq
- GSM7664084 H9 WT D0 RNAseq Replicate 2 H9 WT D0 RNAseq
- GSM7664085 H9 WT D0 RNAseq Replicate 3 H9 WT D0 RNAseq
- GSM7664086 H9 WT D0 RNAseq Replicate 4 H9 WT D0 RNAseq
- GSM7664087 H9 WT D15 RNAseq Replicate 1 H9 WT D15 RNAseq
- GSM7664088 H9 WT D15 RNAseq Replicate 2 H9 WT D15 RNAseq
- GSM7664089 H9 WT D15 RNAseq Replicate 3 H9 WT D15 RNAseq
- GSM7664090 H9 WT D15 RNAseq Replicate 4 H9 WT D15 RNAseq
- GSM7664091 H9 WT D35 RNAseq Replicate 1 H9 WT D35 RNAseq
- GSM7664092 H9 WT D35 RNAseq Replicate 2 H9 WT D35 RNAseq
- GSM7664093 H9 WT D35 RNAseq Replicate 3 H9 WT D35 RNAseq
- GSM7664094 H9 WT D35 RNAseq Replicate 4 H9 WT D35 RNAseq
- GSM7664095 H9 WT D60 RNAseq Replicate 1 H9 WT D60 RNAseq
- GSM7664096 H9 WT D60 RNAseq Replicate 2 H9 WT D60 RNAseq
- GSM7664097 H9 WT D60 RNAseq Replicate 3 H9 WT D60 RNAseq
- GSM7664155 H9 WT D0 H3K27ac Replicate 1 H9 WT D0 H3K27ac
- GSM7664156 H9 WT D0 H3K27ac Replicate 2 H9 WT D0 H3K27ac
- GSM7664157 H9 WT D0 H3K27ac Replicate 3 H9 WT D0 H3K27ac
- GSM7664158 H9 WT D0 H3K27ac Replicate 4 H9 WT D0 H3K27ac
- GSM7664159 H9 WT D0 H3K27ac Replicate 5 H9 WT D0 H3K27ac
- GSM7664160 H9 WT D0 H3K27me3 Replicate 1 H9 WT D0 H3K27me3
- GSM7664161 H9 WT D0 H3K27me3 Replicate 2 H9 WT D0 H3K27me3
- GSM7664162 H9 WT D0 H3K27me3 Replicate 3 H9 WT D0 H3K27me3
- GSM7664163 H9 WT D0 H3K27me3 Replicate 4 H9 WT D0 H3K27me3
- GSM7664164 H9 WT D0 H3K27me3 Replicate 5 H9 WT D0 H3K27me3
- GSM7664165 H9 WT D0 H3K4me3 Replicate 1 H9 WT D0 H3K4me3
- GSM7664166 H9 WT D0 H3K4me3 Replicate 2 H9 WT D0 H3K4me3
- GSM7664167 H9 WT D0 H3K4me3 Replicate 3 H9 WT D0 H3K4me3
- GSM7664168 H9 WT D0 H3K4me3 Replicate 4 H9 WT D0 H3K4me3
- GSM7664169 H9 WT D0 H3K4me3 Replicate 5 H9 WT D0 H3K4me3
- GSM7664170 H9 WT D0 H3K4me3 Replicate 6 H9 WT D0 H3K4me3
- GSM7664171 H9 WT D0 H3K9me3 Replicate 1 H9 WT D0 H3K9me3
- GSM7664172 H9 WT D0 H3K9me3 Replicate 2 H9 WT D0 H3K9me3
- GSM7664173 H9 WT D0 H3K9me3 Replicate 3 H9 WT D0 H3K9me3
- GSM7664174 H9 WT D0 IgG Replicate 1 H9 WT D0 IgG
- GSM7664175 H9 WT D0 IgG Replicate 2 H9 WT D0 IgG
- GSM7664176 H9 WT D0 IgG Replicate 3 H9 WT D0 IgG
- GSM7664177 WT D15-V H3K27ac Replicate 1 WT D15-V H3K27ac
- GSM7664178 WT D15-V H3K27ac Replicate 2 WT D15-V H3K27ac
- GSM7664179 WT D15-V H3K27ac Replicate 3 WT D15-V H3K27ac
+ 78 more — browse all 118 samples with per-sample file links →
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, elements, factors
- GSE275721 Lineage master regulator and cancer-selective partner transcription factors rewire 3D genome topology for tumor-specific gene control 72 samples shares transcription, factors, control
- GSE325670 Promoter mutagenesis and a massively parallel reporter screen of the MAPT locus identifies cis-regulatory elements and genetic variation effects 140 samples shares cis-regulatory, elements
- GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription, factors
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares transcription, factors
- GSE290304 Human CRX Regulates Photoreceptor Cells Development via Bidirectional Transcriptional Control in Retinal Organoids 11 samples shares transcription, control
- GSE196619 Synthetic transcription factor overrides persistent repressive chromatin marks 120 samples shares transcription
- GSE273326 A trimeric USP11-USP7-TCEAL1 complex stabilizes paused RNAPII to sustain oncogenic transcription 63 samples shares transcription
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.