KMT2D regulates Fanconi anemia pathway genes through regulating promoters/enhances upon glucose deprivation (CHIPseq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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
- 14 samples: 12 distinct titles, 2 of them repeatedGroups 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
- Histone-methyltransferase KMT2D deficiency impairs the Fanconi anemia/BRCA pathway upon glycolytic inhibition in squamous cell carcinomaNature communications · 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 GSE234640_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 PRJNA982171 and SRA study SRP442243. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 14 sample titles: 12 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.
- GSM7472489 KD_ct
- GSM7472490 Kin_ct
- GSM7472491 NGWT-H3K4me1
- GSM7472492 NGKO-H3K4me1
- GSM7472493 NGWT-H3K27ac
- GSM7472494 NGKO-H3K27ac
- GSM7472495 NGWT-H3K4me3
- GSM7472496 NGKO-H3K4me3
- GSM7472497 NGWT-H3K27me3
- GSM7472498 NGKO-H3K27me3
- GSM7472499 NGWT-H3K9me3
- GSM7472500 NGKO-H3K9me3
- GSM7472501 NGWT-H3
- GSM7472502 NGKO-H3
- GSE234716 KMT2D regulates gene expression through regulating promoters/enhances upon glucose deprivation. 29 samples shares kmt2d, deprivation, regulating, promoters, enhances, glucose
- GSE237454 Gene regulation profiling by KMT2D under different glucose conditions in HNSCC (RNAseq) 14 samples shares kmt2d, glucose
- GSE223052 TFIIIC and MYCN link the three-dimensional chromatin structure of promoters to transcription termination of stalled RNA polymerase (ChIPseq CnR) 32 samples shares promoters, chipseq
- GSE278896 RNA Polymerase II pausing enhances estrogen receptor-alpha binding on promoters in RNA-dependent manner 22 samples shares promoters, enhances
- GSE317139 Effect of glucose deprivation and silencing of transcription factors ATF4 and ATF6 on gene expression in human lung adenocarcinoma cell line A549 36 samples shares deprivation, glucose
- GSE316477 Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A 11 samples shares regulating, enhances
- GSE246170 Glucose deprivation regulates the expression of BACH1-upregulated pro-metastatic genes 10 samples shares deprivation, glucose
- GSE285790 KMT2D promotes castration-resistant prostate cancer progerssion by reactivating AR via FOXA1 [ChIP-seq, Cut & Tag] 48 samples shares kmt2d
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.