Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
- 10 samples: 5 conditions, mostly in duplicateGroups 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
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 GSE269216_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 PRJNA1120741 and SRA study SRP512151. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 of them. 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 ATAC_BaF3
- GSM8308812 ATAC_BaF3-2 ATAC_BaF3
- GSM8308813 ATAC_961C-1 ATAC_961C
- GSM8308814 ATAC_961C-2 ATAC_961C
- GSM8308815 ATAC_961C_HoxBlinc_KO1 ATAC_961C_HoxBlinc_KO
- GSM8308816 ATAC_961C_HoxBlinc_KO2 ATAC_961C_HoxBlinc_KO
- GSM8308817 ATAC_HoxBlincTg_BALL1 ATAC_HoxBlincTg_BALL
- GSM8308818 ATAC_HoxBlincTg_BALL2 ATAC_HoxBlincTg_BALL
- GSM8308819 ATAC_WT1 ATAC_WT
- GSM8308820 ATAC_WT2 ATAC_WT
- GSE225576 An atlas of the aging mouse transcriptome and proteome reveals the features of age-related post-transcriptional dysregulation 128 samples shares transcription, dysregulation
- GSE273878 Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq] 48 samples shares transcription, reprograms
- GSE276335 Age-like Methylation Changes of HSCs in Gadd45b knock-out mice 29 samples shares hsc
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares transcription
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 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.