APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma
RNA-seq (gene expression) · human · 38 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
- Homo sapiens (human)
- Topic
- Lung cancerThis series is part of our curated briefing on it.
- Samples
- 38 samples: 15 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.
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 GSE245173_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 PRJNA1027291 and SRA study SRP465956. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 15 replicated groups read from 38 sample titles; they account for 36 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.
- GSM7837909 WT_1 WT
- GSM7837910 WT_2 WT
- GSM7837911 AKO_1 AKO
- GSM7837912 AKO_2 AKO
- GSM7837913 A549 WT1 A549 WT
- GSM7837914 A549 WT2 A549 WT
- GSM7837915 A549 WT3 A549 WT
- GSM7837916 A549 AKO1 A549 AKO
- GSM7837917 A549 AKO2 A549 AKO
- GSM7837918 A549 AKO3 A549 AKO
- GSM7837919 H1944 WT1 H1944 WT
- GSM7837920 H1944 WT2 H1944 WT
- GSM7837921 H1944 AKO1 H1944 AKO
- GSM7837922 H1944 AKO2 H1944 AKO
- GSM7837940 fWT_1 fWT
- GSM7837941 fWT_2 fWT
- GSM7837942 fWT_3 fWT
- GSM7837943 fWT_4 fWT
- GSM7837944 ff_1 ff
- GSM7837945 ff_2 ff
- GSM7837946 ff_3 ff
- GSM7837947 fN_1 fN
- GSM7837948 fN_2 fN
- GSM7837949 fN_3 fN
- GSM8383562 ATAC_WT_1 ATAC_WT
- GSM8383563 ATAC_WT__2 ATAC_WT
- GSM8383564 ATAC_AKO_1 ATAC_AKO
- GSM8383565 ATAC_AKO_2 ATAC_AKO
- GSM8385508 H_BG4_WT_1
- GSM8385509 H_BG4_AKO_1
- GSM8385510 A_H3K4me3_WT_1 A_H3K4me3_WT
- GSM8385511 A_H3K4me3_WT__2 A_H3K4me3_WT
- GSM8385512 A_H3K4me3_AKO_1 A_H3K4me3_AKO
- GSM8385513 A_H3K4me3_AKO_2 A_H3K4me3_AKO
- GSM8599667 A_BG4_ARG2MUT_1 A_BG4_ARG2MUT
- GSM8599668 A_BG4_ARG2MUT_2 A_BG4_ARG2MUT
- GSM8599669 A_BG4_CPS1MUT_1 A_BG4_CPS1MUT
- GSM8599670 A_BG4_CPS1MUT_2 A_BG4_CPS1MUT
- GSE10072 Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival 107 samples same disease briefing · shares adenocarcinoma, lung
- GSE17958 Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples. 87 samples same disease briefing · shares 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
- GSE104244 Bone Marrow Derived Macrophages, NSCLC cell lines, and Kras G12D Lung Tumors Treated with Epigenetic Agents 33 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
- 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.