Targeting transcriptional factor YY1 is synthetic lethal with loss of the histone demethylase KDM5C
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- 18 samples: 18 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
- Targeting the transcription factor YY1 is synthetic lethal with loss of the histone demethylase KDM5CEMBO reports · 2024
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 GSE270719_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 PRJNA1128074 and SRA study SRP515964. 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 18 sample titles: 18 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.
- GSM8350597 ACHN_Parental, YY1, ChIP
- GSM8350598 ACHN_OEKDM5C, YY1, ChIP
- GSM8350599 ACHN_OEKDM5C_H514A, YY1, ChIP
- GSM8350600 ACHN_shKDM5C, YY1, ChIP
- GSM8350601 ACHN_Parental, H3K4me3, ChIP
- GSM8350602 ACHN_shKDM5C, H3K4me3, ChIP
- GSM8350603 ACHN_Parental, input, ChIP
- GSM8350604 ACHN_OEKDM5C, input, ChIP
- GSM8350605 ACHN_OEKDM5C_H514A, input, ChIP
- GSM8350606 ACHN_shKDM5C, input, ChIP
- GSM8350607 HK2_Parental, YY1, ChIP
- GSM8350608 HK2_OEKDM5C, YY1, ChIP
- GSM8350609 HK2_OEKDM5C_H514A, YY1, ChIP
- GSM8350610 HK2_shKDM5C, YY1, ChIP
- GSM8350611 HK2_Parental, input, ChIP
- GSM8350612 HK2_OEKDM5C, input, ChIP
- GSM8350613 HK2_OEKDM5C_H514A, input, ChIP
- GSM8350614 HK2_shKDM5C, input, ChIP
- GSE299017 Basis for Lineage-Determining Pioneer Factors Targeting Distinct Repressed Chromatin States 69 samples shares targeting, factor
- GSE269555 Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&RUN] 39 samples shares targeting, histone
- GSE255132 Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer (ChIP-Seq) 38 samples shares targeting, histone
- GSE164456 Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma 69 samples shares demethylase, histone
- GSE331257 Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states [RNA-Seq] 24 samples shares demethylase, histone
- GSE316477 Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A 11 samples shares demethylase, histone
- GSE261011 YY1 stabilizes super enhancer-promoter loops and gene expression during mesenchymal stem cell aging 14 samples shares yy1
- GSE279619 SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation. 124 samples shares targeting
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.