CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 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 pancreatic cancer glutamine dependency confers vulnerability to GPX4-dependent ferroptosisCell reports. Medicine · 2025
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 GSE246545_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 PRJNA1033603 and SRA study SRP469141. 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 12 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.
- GSM7871070 K4me3_sgLacz_Cont
- GSM7871071 K4me3_sgLacz_DON
- GSM7871072 K4me3_sgPaxip1_1_Cont
- GSM7871073 K4me3_sgPaxip1_1_DON
- GSM7871074 K4me3_sgPaxip1_3_Cont
- GSM7871075 K4me3_sgPaxip1_3_DON
- GSM7871076 Paxip1_sgLacz_Cont
- GSM7871077 Paxip1_sgLacz_DON
- GSM7871078 Paxip1_sgPaxip1_1_Cont
- GSM7871079 Paxip1_sgPaxip1_1_DON
- GSM7871080 Paxip1_sgPaxip1_3_Cont
- GSM7871081 Paxip1_sgPaxip1_3_DON
- GSE222133 CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line 12 samples shares h3k4me3, kpc1199, pdac, cut
- GSE229903 CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line 10 samples shares h3k4me3, kpc1199, pdac, cut
- GSE289600 CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [Cut&Tag] 52 samples shares h3k4me3, cut
- GSE319420 Uncovering Critical Lysines in Mammalian Histone H3 with High-Throughput CRISPR Prime Editing [CUT&Tag] 26 samples shares crispr, cut
- GSE261412 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ] 24 samples shares h3k4me3, cut
- GSE255571 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 [Mouse CUT&Tag] 10 samples shares h3k4me3, cut
- GSE273667 Genome-wide CRISPR screening identifies the E3 ubiquitin ligase HERC1 as a modulator of the response to nucleoside analogs in acute myeloid leukemia 12 samples shares crispr, cut
- GSE324386 Transcriptomic profiling of CRISPR-Cas9 knockout of RAD51D, LIMCH1, and BRD9 in MC38 colorectal cancer cells reveals regulation of PD-L1 expression 29 samples shares crispr, knockout
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.