Loss of tumor suppressors promotes a non-cell-autonomous inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
- 24 samples: 12 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
- Loss of tumor suppressors promotes inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppressionNature communications · 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 GSE249972_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 PRJNA1051520 and SRA study SRP477524. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7968258 ATAC_4T1-C1, rep1 ATAC_4T1-C1,
- GSM7968259 ATAC_4T1-C1, rep2 ATAC_4T1-C1,
- GSM7968260 ATAC_4T1-sgNf1, rep1 ATAC_4T1-sgNf1,
- GSM7968261 ATAC_4T1-sgNf1, rep2 ATAC_4T1-sgNf1,
- GSM7968262 ATAC_4T1-sgTsc1, rep1 ATAC_4T1-sgTsc1,
- GSM7968263 ATAC_4T1-sgTsc1, rep2 ATAC_4T1-sgTsc1,
- GSM7968264 ATAC_4T1-sgTgfbr2, rep1 ATAC_4T1-sgTgfbr2,
- GSM7968265 ATAC_4T1-sgTgfbr2, rep2 ATAC_4T1-sgTgfbr2,
- GSM7968272 Cas_PT_4T1-C1, rep1 Cas_PT_4T1-C1,
- GSM7968273 Cas_PT_4T1-C1, rep2 Cas_PT_4T1-C1,
- GSM7968274 Cas_PT_4T1-sgNf1, rep1 Cas_PT_4T1-sgNf1,
- GSM7968275 Cas_PT_4T1-sgNf1, rep2 Cas_PT_4T1-sgNf1,
- GSM7968276 Cas_PT_4T1-sgTgfbr2, rep1 Cas_PT_4T1-sgTgfbr2,
- GSM7968277 Cas_PT_4T1-sgTgfbr2, rep2 Cas_PT_4T1-sgTgfbr2,
- GSM7968278 Cas_PT_4T1-sgTsc1, rep1 Cas_PT_4T1-sgTsc1,
- GSM7968279 Cas_PT_4T1-sgTsc1, rep2 Cas_PT_4T1-sgTsc1,
- GSM7968284 vitro_4T1-C1, rep1 vitro_4T1-C1,
- GSM7968285 vitro_4T1-C1, rep2 vitro_4T1-C1,
- GSM7968286 vitro_4T1-sgNf1, rep1 vitro_4T1-sgNf1,
- GSM7968287 vitro_4T1-sgNf1, rep2 vitro_4T1-sgNf1,
- GSM7968288 vitro_4T1-sgTgfbr2, rep1 vitro_4T1-sgTgfbr2,
- GSM7968289 vitro_4T1-sgTgfbr2, rep2 vitro_4T1-sgTgfbr2,
- GSM7968290 vitro_4T1-sgTsc1, rep1 vitro_4T1-sgTsc1,
- GSM7968291 vitro_4T1-sgTsc1, rep2 vitro_4T1-sgTsc1,
- GSE243170 LTBR-mediated immunomodulation of the tumor microenvironment promotes anti-tumor responses 20 samples shares microenvironment, promotes, mediated
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment, promotes
- GSE218173 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid] 150 samples shares microenvironment, promotes
- GSE218177 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [drug] 33 samples shares microenvironment, promotes
- GSE240371 Targeting IRE1α reprograms the tumor microenvironment and enhances anti-tumor immunity in prostate cancer [RNA-Seq] 21 samples shares microenvironment, enhances
- GSE319318 Inactivation of CDKN2A-ARF Promotes p53-Independent Remodeling of the PDAC Tumor Microenvironment [RNA-Seq] 20 samples shares microenvironment, promotes
- GSE288530 Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis 18 samples shares microenvironment, suppression
- GSE298273 Tumor-derived RAC1A159V mutation promotes an immunosuppressive tumor microenvironment that represses response to immune checkpoint inhibitor [RNA-Seq] 12 samples shares microenvironment, promotes
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.