ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 46 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
- 46 samples: 46 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
- ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotencyNature communications · 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 GSE270948_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 PRJNA1129101 and SRA study SRP516673. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 1 samples read as cases, 14 as controls.
How we read this: Read from 46 sample titles: 46 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.
- GSM8365540 UCLA1 primed hESC, WT +sgNT, rep1 (ATAC-seq)
- GSM8365541 UCLA1 primed hESC, WT +sgNT, rep2 (ATAC-seq)
- GSM8365542 UCLA1 primed hESC, WT +sgNT, rep3 (ATAC-seq)
- GSM8365543 UCLA1 primed hESC, WT +sgZIC2, rep1 (ATAC-seq)
- GSM8365544 UCLA1 primed hESC, WT +sgZIC2, rep2 (ATAC-seq)
- GSM8365545 UCLA1 primed hESC, WT +sgZIC2, rep3 (ATAC-seq)
- GSM8365546 UCLA1 primed hESC, ZIC3-/- +sgNT, rep1 (ATAC-seq)
- GSM8365547 UCLA1 primed hESC, ZIC3-/- +sgNT, rep2 (ATAC-seq)
- GSM8365548 UCLA1 primed hESC, ZIC5-/- +sgNT, rep1 (ATAC-seq)
- GSM8365549 UCLA1 primed hESC, ZIC5-/- +sgNT, rep2 (ATAC-seq)
- GSM8365550 UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep1 (ATAC-seq)
- GSM8365551 UCLA1 primed hESC, ZIC3-/- +sgZIC2, rep2 (ATAC-seq)
- GSM8365552 UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep1 (ATAC-seq)
- GSM8365553 UCLA1 primed hESC, ZIC5-/- +sgZIC2, rep2 (ATAC-seq)
- GSM8365554 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep1 (ATAC-seq)
- GSM8365555 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep2 (ATAC-seq)
- GSM8365556 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgNT, rep3 (ATAC-seq)
- GSM8365557 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep1 (ATAC-seq)
- GSM8365558 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep2 (ATAC-seq)
- GSM8365559 UCLA1 primed hESC, ZIC3-/-ZIC5-/- +sgZIC2, rep3 (ATAC-seq)
- GSM8365560 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep1 (ATAC-seq)
- GSM8365561 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep2 (ATAC-seq)
- GSM8365562 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep3 (ATAC-seq)
- GSM8365563 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DMSO, rep4 (ATAC-seq)
- GSM8365564 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep1 (ATAC-seq)
- GSM8365565 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep2 (ATAC-seq)
- GSM8365566 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep3 (ATAC-seq)
- GSM8365567 UCLA1 ZIC3-/- naïve hESC, inducible ZIC2, DOX 72h, rep4 (ATAC-seq)
- GSM8365568 UCLA1 reverting hESC, NT, 5iLAF d6, rep1 (ATAC-seq)
- GSM8365569 UCLA1 reverting hESC, NT, 5iLAF d6, rep2 (ATAC-seq)
- GSM8365570 UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep1 (ATAC-seq)
- GSM8365571 UCLA1 reverting hESC, ZIC3-/-, 5iLAF d6, rep2 (ATAC-seq)
- GSM8365572 UCLA1 naïve hESC, inducible ZIC2, DMSO, untreated (ATAC-seq)
- GSM8365573 UCLA1 naïve hESC, inducible ZIC2, DMSO, ACBI1-treated (ATAC-seq)
- GSM8365574 UCLA1 naïve hESC, inducible ZIC2, DOX, untreated (ATAC-seq)
- GSM8365575 UCLA1 naïve hESC, inducible ZIC2, DOX, ACBI1-treated (ATAC-seq)
- GSM8365576 UCLA1 naïve hESC, inducible ZIC2, DMSO, rep1 (ATAC-seq)
- GSM8365577 UCLA1 naïve hESC, inducible ZIC2, DMSO, rep2 (ATAC-seq)
- GSM8365578 UCLA1 naïve hESC, inducible ZIC2, DOX, rep1 (ATAC-seq)
- GSM8365579 UCLA1 naïve hESC, inducible ZIC2, DOX, rep2 (ATAC-seq)
+ 6 more — browse all 46 samples with per-sample file links →
- GSE270784 ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq] 107 samples shares zic2, zic3, swi, snf, pluripotency, recruitment, progression, safeguard
- GSE270787 ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency 205 samples shares zic2, zic3, swi, snf, pluripotency, recruitment, progression, safeguard
- GSE180483 PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [ChIP-seq] 88 samples shares swi, snf, progression
- GSE261988 SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [ChIP-Seq] 79 samples shares swi, snf, progression
- GSE180487 PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression 137 samples shares swi, snf, progression
- GSE180481 PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [RNA-seq] 38 samples shares swi, snf, progression
- GSE299672 PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers [ChIP-seq] 132 samples shares swi, snf
- GSE256316 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity [ChIP-Seq] 121 samples shares swi, snf
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.