Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors [dataset 1]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 65 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
- 65 samples: 65 samples, each with a distinct title — no replicated groupsGroups 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
- Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratificationCancer cell · 2021
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 GSE255330_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 PRJNA1074689 and SRA study SRP488933. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 43 samples read as cases, 3 as controls.
How we read this: Read from 65 sample titles: 65 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.
- GSM8069361 Bone marrow of naive mice replicate 1 (scATAC-seq)
- GSM8069362 Bone marrow of tumor-bearing (KP) mice replicate 1 (scATAC-seq)
- GSM8069363 Bone marrow of tumor-bearing (KP) mice replicate 2 (scATAC-seq)
- GSM8069364 Lung of naive mice (scATAC-seq)
- GSM8069365 Lung of tumor-bearing (KP) mice replicate 1 (scATAC-seq)
- GSM8069366 Blood of tumor-bearing (KP) mice (scATAC-seq)
- GSM8069367 PBMCs from NSCLC Patient Lu881 (scATAC-seq)
- GSM8069368 PBMCs from NSCLC Patient Lu883 (scATAC-seq)
- GSM8069369 PBMCs from NSCLC Patient Lu895 (scATAC-seq)
- GSM8069370 PBMCs from NSCLC Patient Lu898 (scATAC-seq)
- GSM8069371 PBMCs from NSCLC Patient Lu912 (scATAC-seq)
- GSM8069372 PBMCs from NSCLC Patient Lu929 (scATAC-seq)
- GSM8069373 PBMCs from NSCLC Patient Lu931 (scATAC-seq)
- GSM8069374 PBMCs from NSCLC Patient Lu934 (scATAC-seq)
- GSM8069375 PBMCs from NSCLC Patient Lu936 (scATAC-seq)
- GSM8069376 Tumor cells from NSCLC Patient Lu881 (scATAC-seq)
- GSM8069377 Tumor cells from NSCLC Patient Lu883 (scATAC-seq)
- GSM8069378 Tumor cells from NSCLC Patient Lu895 (scATAC-seq)
- GSM8069379 Tumor cells from NSCLC Patient Lu898 (scATAC-seq)
- GSM8069380 Tumor cells from NSCLC Patient Lu912 (scATAC-seq)
- GSM8069381 Tumor cells from NSCLC Patient Lu929 (scATAC-seq)
- GSM8069382 Tumor cells from NSCLC Patient Lu931 (scATAC-seq)
- GSM8069383 Tumor cells from NSCLC Patient Lu934 (scATAC-seq)
- GSM8069384 Tumor cells from NSCLC Patient Lu936 (scATAC-seq)
- GSM8069385 Adjacent normal Patient Lung cells from NSCLC Patient Lu881 (scATAC-seq)
- GSM8069386 Adjacent normal Patient Lung cells from NSCLC Patient Lu883 (scATAC-seq)
- GSM8069387 Adjacent normal Patient Lung cells from NSCLC Patient Lu895 (scATAC-seq)
- GSM8069388 Adjacent normal Patient Lung cells from NSCLC Patient Lu898 (scATAC-seq)
- GSM8069389 Adjacent normal Patient Lung cells from NSCLC Patient Lu912 (scATAC-seq)
- GSM8069390 Adjacent normal Patient Lung cells from NSCLC Patient Lu929 (scATAC-seq)
- GSM8069391 Adjacent normal Patient Lung cells from NSCLC Patient Lu931 (scATAC-seq)
- GSM8069392 Adjacent normal Patient Lung cells from NSCLC Patient Lu934 (scATAC-seq)
- GSM8069393 Adjacent normal Patient Lung cells from NSCLC Patient Lu936 (scATAC-seq)
- GSM8069394 PBMCs from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])
- GSM8069395 PBMCs from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])
- GSM8069396 PBMCs from NSCLC Patient Lu954 ATAC (Multiome [RNA + ATAC])
- GSM8069397 PBMCs from NSCLC Patient Lu979 ATAC (Multiome [RNA + ATAC])
- GSM8069398 Tumor cells from NSCLC Patient Lu927 ATAC (Multiome [RNA + ATAC])
- GSM8069399 Tumor cells from NSCLC Patient Lu941 ATAC (Multiome [RNA + ATAC])
- GSM8069400 Tumor cells from NSCLC Patient Lu952 ATAC (Multiome [RNA + ATAC])
+ 25 more — browse all 65 samples with per-sample file links →
- GSE281956 Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia. 59 samples shares dysregulation, myeloid
- GSE152277 G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT 30 samples shares immunosuppressive, myeloid
- GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis 166 samples shares progenitor
- GSE217639 Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor 49 samples shares progenitor
- GSE243020 The loss of an orphan nuclear receptor NR2E3 augments Wnt/β-Catenin signaling via epigenetic dysregulation that promotes the Sp1-β catenin-p300 interactions in hepatocellular carcinoma. 8 samples shares dysregulation
- GSE217847 IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer 136 samples shares macrophages
- GSE269031 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages 92 samples shares macrophages
- GSE285158 Charting the transition from in vitro production through in vivo diversification of human glial progenitor cells 72 samples shares progenitor
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.