KLF4 promotes a KRT13+ hillock-like state in squamous lung cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 55 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)
- Topic
- Lung cancerThis series is part of our curated briefing on it.
- Samples
- 55 samples: 55 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.
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 GSE291730_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 PRJNA1235148 and SRA study SRP567040. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 55 sample titles: 55 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.
- GSM8821088 BEAS-2B_TRE-KLF4_dox
- GSM8821089 BEAS-2B_TRE-KLF4_no_dox
- GSM8821090 KP 11139X10, CMV-Cre, replicate 1
- GSM8821091 KP 11139X15, CMV-Cre, replicate 2
- GSM8821092 KP 11139X16, CMV-Cre, replicate 3
- GSM8821093 KP 11139X26, CMV-Cre, replicate 4
- GSM8821094 KP 11139X27, CMV-Cre, replicate 5
- GSM8821095 KP 11139X29, CMV-Cre, replicate 6
- GSM8821096 KP 11139X3, CMV-Cre, replicate 7
- GSM8821097 KP 11139X4, CMV-Cre, replicate 8
- GSM8821098 LP 13820X1, CMV-Cre, replicate 1
- GSM8821099 LP 13820X2, CMV-Cre, replicate 2
- GSM8821100 LP 13820X3, CMV-Cre, replicate 3
- GSM8821101 LP 13820X4, CMV-Cre, replicate 4
- GSM8821102 LP 13820X5, CMV-Cre, replicate 5
- GSM8821103 LP 13820X6, CMV-Cre, replicate 6
- GSM8821104 RPM 12135X1, CGRP-Cre, replicate 1
- GSM8821105 RPM 12135X10, CGRP-Cre, replicate 2
- GSM8821106 RPM 12135X11, CGRP-Cre, replicate 3
- GSM8821107 RPM 12135X3, CGRP-Cre, replicate 4
- GSM8821108 RPM 12135X4, CGRP-Cre, replicate 5
- GSM8821109 RPM 12135X5, CGRP-Cre, replicate 6
- GSM8821110 RPM 12135X6, CGRP-Cre, replicate 7
- GSM8821111 RPM 12135X7, CGRP-Cre, replicate 8
- GSM8821112 RPM 12135X8, CGRP-Cre, replicate 9
- GSM8821113 RPM 12135X9, CGRP-Cre, replicate 10
- GSM8821114 RPM 12135X2, CMV-Cre, replicate 1
- GSM8821115 RPM 17536X10, CMV-Cre, replicate 2
- GSM8821116 RPM 17536X11, CMV-Cre, replicate 3
- GSM8821117 RPM 17536X12, CMV-Cre, replicate 4
- GSM8821118 RPM 17536X9, CMV-Cre, replicate 5
- GSM8821119 RPR2 16080X3, CGRP-Cre, replicate 1
- GSM8821120 RPR2 16080X4, CGRP-Cre, replicate 2
- GSM8821121 RPR2 17536X1, CGRP-Cre, replicate 3
- GSM8821122 RPR2 17536X2, CGRP-Cre, replicate 4
- GSM8821123 RPR2 17536X3, CGRP-Cre, replicate 5
- GSM8821124 RPR2 12416X7, CMV-Cre, replicate 1
- GSM8821125 RPR2 12416X8, CMV-Cre, replicate 2
- GSM8821126 RPR2 16080X1, CMV-Cre, replicate 3
- GSM8821127 RPR2 16080X2, CMV-Cre, replicate 4
+ 15 more — browse all 55 samples with per-sample file links →
- GSE17958 Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples. 87 samples same disease briefing · shares squamous, lung
- GSE114761 Transforming Growth Factor β-Induced Epithelial-to-Mesenchymal Signature Predicts Metastasis-Free Survival in Non-Small Cell Lung Cancer. 42 samples same disease briefing · shares lung
- GSE127465 Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species 40 samples same disease briefing · shares lung
- GSE103550 Lung Cancer Cell-Mediated Skeletal Muscle Mitochondrial Dysfunction is Mitigated by 1a,25-Dihydroxyvitamin D3 24 samples same disease briefing · shares lung
- GSE241518 High-throughout sequencing of colorectal cancer and non-small cell lung cancer cells treated actived compound YHM18 4 samples same disease briefing · shares lung
- GSE10072 Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival 107 samples same disease briefing · shares lung
- GSE104244 Bone Marrow Derived Macrophages, NSCLC cell lines, and Kras G12D Lung Tumors Treated with Epigenetic Agents 33 samples same disease briefing · shares lung
- GSE27389 Substitutions in the KRas oncogene determine protein behavior: Implications for signaling and clinical outcome. 22 samples same disease briefing
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.