Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [RNA-Seq]
RNA-seq (gene expression) · mouse · 20 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
- 20 samples: 7 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 GSE269226_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 PRJNA1120762 and SRA study SRP512997. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 7 replicated groups read from 20 sample titles; they account for 18 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.
- GSM8308920 RNA_BaF3-1 RNA_BaF3
- GSM8308921 RNA_BaF3-2 RNA_BaF3
- GSM8308922 RNA_961C-1 RNA_961C
- GSM8308923 RNA_961C-2 RNA_961C
- GSM8308924 RNA_961C-3 RNA_961C
- GSM8308925 RNA_961C_HoxBlinc_KO1 RNA_961C_HoxBlinc_KO
- GSM8308926 RNA_961C_HoxBlinc_KO2 RNA_961C_HoxBlinc_KO
- GSM8308927 RNA_961C_HoxBlinc_KO3 RNA_961C_HoxBlinc_KO
- GSM8308928 RNA_961C_HoxBlinc_KO4 RNA_961C_HoxBlinc_KO
- GSM8308929 RNA_A1929_WT1 RNA_A1929_WT
- GSM8308930 RNA_A1929_WT2 RNA_A1929_WT
- GSM8308931 RNA_A1929_HoxBlinc_KO1 RNA_A1929_HoxBlinc_KO
- GSM8308932 RNA_A1929_HoxBlinc_KO2 RNA_A1929_HoxBlinc_KO
- GSM8308933 RNA_A1929_HoxBlinc_KO3 RNA_A1929_HoxBlinc_KO
- GSM8308934 RNA_1265_WT
- GSM8308935 RNA_1265_HOXBLINC_KD1 RNA_1265_HOXBLINC_KD
- GSM8308936 RNA_1265_HOXBLINC_KD2 RNA_1265_HOXBLINC_KD
- GSM8308937 RNA_1292_WT
- GSM8308938 RNA_1292_HOXBLINC_KD1 RNA_1292_HOXBLINC_KD
- GSM8308939 RNA_1292_HOXBLINC_KD2 RNA_1292_HOXBLINC_KD
- GSE255808 Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 47 samples shares nup98, transcription
- GSE297415 Harnessing the E3 ligase SPOP for targeted degradation of the NUP98::KDM5A fusion oncoprotein 17 samples shares nup98
- GSE283532 MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia 70 samples shares nup98
- GSE202126 Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors 1089 samples shares transcription
- GSE102556 Sex-specific Transcriptional Signatures in Human Depression 341 samples shares transcription
- GSE260456 DOT1L provides transcriptional memory through PRC1.1 antagonism [RNA-seq] 180 samples shares transcription
- GSE218715 EZH2 gain-of-function mutations distort H3K27me3 landscapes and transform transcriptional responses to PRC2 inhibition [RNA-seq] 88 samples shares transcription
- GSE255108 Targeting CDK7 function in the RNA Polymerase II transcription cycle in inflammatory arthritis 64 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.