Effect of conditional triple-knockout of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c or overexpression of KDM4C/JMJD2C mutants with different phase separation ability on gene expression in mouse embryonic stem cells. [RNA-Seq]
RNA-seq (gene expression) · mouse · 10 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 8 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
- JMJD2 regulates enhancer-promoter interactions via biomolecular condensate formationNature genetics · 2026
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 GSE232844_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA974058 and SRA study SRP438533. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 8 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.
- GSM7384457 RNAseq_mESC_Ctrl_R1
- GSM7384458 RNAseq_mESC_Ctrl_R2
- GSM7384459 RNAseq_mESC_JMJD2_TKO_R1
- GSM7384460 RNAseq_mESC_JMJD2_TKO_R2
- GSM7384461 RNAseq_mESC_JMJD2C_FL_OE
- GSM7384462 RNAseq_mESC_JMJD2C_Mut_OE
- GSM7384463 RNAseq_mESC_JMJD2C_Mut_hIDR1_OE
- GSM7384464 RNAseq_mESC_hIDR1_OE
- GSM7384465 RNAseq_mESC_JMJD2C_Mut_hIDR2_OE
- GSM7384466 RNAseq_mESC_hIDR2_OE
- GSE232845 Effect of conditional triple-knockout of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c or overexpression of KDM4C/JMJD2C mutants with different phase separation ability on gene expression in mouse embryonic stem cells. [ChIP-Seq] 46 samples shares jmjd2a, jmjd2b, jmjd2c, kdm4a, kdm4b, kdm4c, triple-knockout, overexpression
- GSE269325 Kdm4a is an activity downregulated barrier to generate engrams for memory separation 6 samples shares kdm4a
- GSE227717 Effect of Kdm4a knockdown (KD) on gene expression in mosue PTR NEPC cells derived from Pb-Cre+,Pten f/f, Trp53 f/f, Rb1 f/f NEPC mouse model 6 samples shares kdm4a
- GSE251753 ETV2/ER71 regulates hematovascular lineage generation and vascularization through an H3K9 demethylase, KDM4A 30 samples shares kdm4a
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.