A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
- 15 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
- A lactate-SREBP2 signaling axis drives tolerogenic dendritic cell maturation and promotes cancer progressionScience immunology · 2024
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 GSE253593_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 PRJNA1066322 and SRA study SRP484546. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 2 as controls.
How we read this: 5 replicated groups read from 15 sample titles; they account for 11 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.
- GSM8023905 Ctrl_LN_CITE
- GSM8023906 TDLN_CITE
- GSM8023907 Tumor_CITE
- GSM8023908 LN0 LN
- GSM8023909 LN1 LN
- GSM8023910 LN2 LN
- GSM8023911 TDLN_DC_scATACseq_Sample_1 TDLN_DC_scATACseq_Sample
- GSM8023912 TDLN_DC_scATACseq_Sample_2 TDLN_DC_scATACseq_Sample
- GSM8023913 human_scRNAseq_tdln1 human_scRNAseq_tdln
- GSM8023914 human_scRNAseq_tdln2 human_scRNAseq_tdln
- GSM8023939 Tumor draining lymph node 1 Tumor draining lymph no…
- GSM8023940 Non Draining lymph node 1 Non Draining lymph node
- GSM8023941 Tumor draining lymph node 2 Tumor draining lymph no…
- GSM8023942 Non Draining lymph node 2 Non Draining lymph node
- GSM8023943 control lymph node
- GSE99311 Enhancer reprogramming promotes pancreatic cancer progression and metastasis 136 samples shares progression, program
- GSE97442 Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia 80 samples shares progression, genetic
- GSE282171 Depression and Anxiety-Induced Metabolic Reprogramming Promotes Hepatocellular Carcinoma Progression through CBX5 Lactylation: Involvement of Taurocholate and PHGDH-Mediated Ferroptosis 28 samples shares progression, program
- GSE324714 Acquired genetic and cell state changes in IDH-mutant glioma progression [coculture experiments] 16 samples shares progression, genetic
- GSE241602 Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression 30 samples shares progression
- GSE277368 The functional antagonism between SIRT2 and MOF regulates cell cycle progression and genome stability [RNA-seq] 18 samples shares progression
- GSE245730 HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [ATAC-seq] 16 samples shares progression
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.