HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 61 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
- 61 samples: 44 distinct titles, 13 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
- HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98-rearranged leukemiaThe Journal of clinical investigation · 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 GSE269258_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 PRJNA1120835 and SRA study SRP512151. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 61 sample titles: 44 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.
- GSM8308811 ATAC_BaF3-1
- GSM8308812 ATAC_BaF3-2
- GSM8308813 ATAC_961C-1
- GSM8308814 ATAC_961C-2
- GSM8308815 ATAC_961C_HoxBlinc_KO1
- GSM8308816 ATAC_961C_HoxBlinc_KO2
- GSM8308817 ATAC_HoxBlincTg_BALL1
- GSM8308818 ATAC_HoxBlincTg_BALL2
- GSM8308819 ATAC_WT1
- GSM8308820 ATAC_WT2
- GSM8308821 ChIP_961C_CTCF
- GSM8308822 ChIP_961C_HoxBlinc_KO_CTCF
- GSM8308823 ChIP_961C_NUP98-PHF23-V5
- GSM8308824 ChIP_961C_HoxBlinc_KO_NUP98-PHF23-V5
- GSM8308825 ChIP_961C_MLL1
- GSM8308826 ChIP_961C_HoxBlinc_KO_MLL1
- GSM8308827 ChIP_961C_IgG
- GSM8308828 ChIP_961C_HoxBlinc_KO_IgG
- GSM8308829 HiC_BaF3
- GSM8308830 HiC_961C
- GSM8308831 HiC_961C_HoxBlinc_KO
- GSM8308832 HiC_WT
- GSM8308833 HiC_HoxBlincTg_BALL
- GSM8308834 scRNA_WT_LK
- GSM8308835 scRNA_HoxBlincTg_LK
- GSM8308859 CnR_BaF3_H3K4me3
- GSM8308860 CnR_961C_H3K4me3
- GSM8308861 CnR_961C_H3K4me3_2
- GSM8308862 CnR_961C_HoxBlinc_KO_H3K4me3
- GSM8308863 CnR_BaF3_IgG
- GSM8308864 CnR_961C_IgG
- GSM8308865 CnR_961C_IgG_2
- GSM8308866 CnR_961C_HoxBlinc_KO_IgG
- GSM8308884 ChIRP_BaF3_LaCZ
- GSM8308885 ChIRP_BaF3_HoxBlinc
- GSM8308886 ChIRP_961C_LaCZ
- GSM8308887 ChIRP_961C_HoxBlinc
- GSM8308888 ChIRP_961C_HoxBlinc_KO_LaCZ
- GSM8308889 ChIRP_961C_HoxBlinc_KO_HoxBlinc
- GSM8308920 RNA_BaF3-1
+ 21 more — browse all 61 samples with per-sample file links →
- GSE255802 Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (Cut&Tag) 20 samples shares nup98, transcription
- GSE267491 Inhibition of DEK contributes to the tolerance of replication stress and restores HSC function in Fanconi anemia 91 samples shares hsc
- GSE283531 MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq] 54 samples shares nup98
- GSE283096 The histone acetyltransferase MOZ is a molecular dependency and therapeutic target in NUP98-rearranged acute myeloid leukemia [WGS, ATACseq, CUT&RUN, scRNAseq] 38 samples shares nup98
- GSE226204 Neurological Cockayne Syndrome Results from R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation 37 samples shares transcription
- GSE289420 Astrocyte-derived cholesterol drives synaptic gene expression in developing neurons and reciprocal astrocytic transcriptional programs 416 samples shares transcription
- GSE261351 Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples 278 samples shares transcription
- GSE241338 Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation 250 samples shares transcription
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.