Extensive binding of uncharacterized human transcription factors to genomic dark matter
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 1028 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
- 1028 samples: 1028 samples, each with a distinct title — no replicated groupsGroups 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
- Extensive binding of uncharacterized human transcription factors to genomic dark matterbioRxiv : the preprint server for biology · 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 GSE280248_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 PRJNA1177443. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from the first 400 of 1028 sample titles: 400 distinct titles with little repetition. 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.
- GSM8589641 ChIP-seq analysis of ZNF367 genomic target locations in HEK293, THC0045TSNN_ZNF367_ChIP1
- GSM8589642 ChIP-seq analysis of ZNF367 genomic target locations in HEK293, THC0046TSNN_ZNF367_ChIP2
- GSM8589643 ChIP-seq analysis of ADNP2 genomic target locations in HEK293, THC0070TANN_ADNP2_ChIP1
- GSM8589645 ChIP-seq analysis of SP140L genomic target locations in HEK293, THC0072TANN_SP140L_ChIP1
- GSM8589646 ChIP-seq analysis of ZBED9 genomic target locations in HEK293, THC0073TANN_ZBED9_ChIP1
- GSM8589647 ChIP-seq analysis of ZBTB47 genomic target locations in HEK293, THC0074TANN_ZBTB47_ChIP1
- GSM8589648 ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0075TANN_ZNF428_ChIP1
- GSM8589649 ChIP-seq analysis of ZSCAN12 genomic target locations in HEK293, THC0076TANN_ZSCAN12_ChIP2
- GSM8589650 ChIP-seq analysis of ZSCAN2 genomic target locations in HEK293, THC0077TANN_ZSCAN2_ChIP1
- GSM8589651 ChIP-seq analysis of ZNF215 genomic target locations in HEK293, THC0078TANN_ZNF215_ChIP2
- GSM8589652 ChIP-seq analysis of ZBTB41 genomic target locations in HEK293, THC0079TANN_ZBTB41_ChIP1
- GSM8589653 ChIP-seq analysis of YY1 genomic target locations in HEK293, THC0080TANN_YY1_ChIP1
- GSM8589654 ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0081TANN_ZBED5_ChIP2
- GSM8589655 ChIP-seq analysis of ZNF428 genomic target locations in HEK293, THC0082TANN_ZNF428_ChIP2
- GSM8589656 ChIP-seq analysis of ZBED5 genomic target locations in HEK293, THC0083TANN_ZBED5_ChIP1
- GSM8589657 ChIP-seq analysis of TERB1 genomic target locations in HEK293, THC0084TANN_TERB1_ChIP2
- GSM8589658 ChIP-seq analysis of RFX5 genomic target locations in HEK293, THC0085TANN_RFX5_ChIP1
- GSM8589659 ChIP-seq analysis of PEG3 genomic target locations in HEK293, THC0086TANN_PEG3_ChIP2
- GSM8589660 ChIP-seq analysis of DNTTIP1 genomic target locations in HEK293, THC0087TANN_DNTTIP1_ChIP2
- GSM8589661 ChIP-seq analysis of GLYR1 genomic target locations in HEK293, THC0088TANN_GLYR1_ChIP2
- GSM8589662 ChIP-seq analysis of SP140L genomic target locations in HEK293, THC0090TANN_SP140L_ChIP2
- GSM8589663 ChIP-seq analysis of THYN1 genomic target locations in HEK293, THC0092TANN_THYN1_ChIP2
- GSM8589664 ChIP-seq analysis of ZBED2 genomic target locations in HEK293, THC0099TANN_ZBED2_ChIP1
- GSM8589665 ChIP-seq analysis of RFX8 genomic target locations in HEK293, THC0100TANN_RFX8_CHIP2
- GSM8589666 ChIP-seq analysis of ZBED2 genomic target locations in HEK293, THC0101TANN_ZBED2_ChIP2
- GSM8589667 ChIP-seq analysis of ZNF318 genomic target locations in HEK293, THC0102TANN_ZNF318_ChIP1
- GSM8589668 ChIP-seq analysis of AKAP8 genomic target locations in HEK293, THC0103TANN_AKAP8_CHIP2
- GSM8589669 ChIP-seq analysis of TIGD3 genomic target locations in HEK293, THC0104TANN_TIGD3_ChIP1
- GSM8589670 ChIP-seq analysis of ZSCAN18 genomic target locations in HEK293, THC0105TANN_ZSCAN18_ChIP2
- GSM8589671 ChIP-seq analysis of SMYD3 genomic target locations in HEK293, THC0106TANN_SMYD3_ChIP1
- GSM8589672 ChIP-seq analysis of ZSCAN12 genomic target locations in HEK293, THC0107TANN_ZSCAN12_ChIP1
- GSM8589673 ChIP-seq analysis of AKAP8 genomic target locations in HEK293, THC0108TANN_AKAP8_CHIP1
- GSM8589674 ChIP-seq analysis of ANKZF1 genomic target locations in HEK293, THC0109TANN_ANKZF1_CHIP2
- GSM8589676 ChIP-seq analysis of ZNF318 genomic target locations in HEK293, THC0111TANN_ZNF318_ChIP2
- GSM8589677 ChIP-seq analysis of ZSCAN4 genomic target locations in HEK293, THC0112TANN_ZSCAN4_ChIP1
- GSM8589679 ChIP-seq analysis of ZBTB47 genomic target locations in HEK293, THC0114TANN_ZBTB47_ChIP2
- GSM8589680 ChIP-seq analysis of ZBED9 genomic target locations in HEK293, THC0116TANN_ZBED9_ChIP2
- GSM8589681 ChIP-seq analysis of BATF2 genomic target locations in HEK293, THC0117TANN_BATF2_CHIP2
- GSM8589682 ChIP-seq analysis of BATF2 genomic target locations in HEK293, THC0118TANN_BATF2_CHIP1
- GSM8589683 ChIP-seq analysis of ZNF215 genomic target locations in HEK293, THC0119TANN_ZNF215_ChIP1
+ 988 more — browse all 1028 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, factors
- GSE293334 Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ChIP-seq] 60 samples shares transcription, factors
- GSE303478 Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome 217 samples shares transcription, extensive
- GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription, 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
- GSE171817 SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin 30 samples shares transcription, binding
- GSE238114 ABI1 regulates transcriptional activity of Androgen Receptor by novel DNA and AR binding mechanism 25 samples shares transcription, binding
- GSE284519 TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination [ChIP-seq] 93 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.