Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer
RNA-seq (gene expression) · human · 16 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)
- Samples
- 16 samples
- 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 GSE126044_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 PRJNA520852 and SRA study SRP183455. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run RNA-seq_Dis_01 … RNA-seq_Dis_08 and carry no group information.
- GSM3589673 RNA-seq_Dis_01
- GSM3589674 RNA-seq_Dis_02
- GSM3589675 RNA-seq_Dis_11
- GSM3589676 RNA-seq_Dis_12
- GSM3589677 RNA-seq_Dis_15
- GSM3589678 RNA-seq_Dis_04
- GSM3589679 RNA-seq_Dis_16
- GSM3589680 RNA-seq_Dis_17
- GSM3589681 RNA-seq_Dis_03
- GSM3589682 RNA-seq_Dis_10
- GSM3589683 RNA-seq_Dis_06
- GSM3589684 RNA-seq_Dis_18
- GSM3589685 RNA-seq_Dis_09
- GSM3589686 RNA-seq_Dis_05
- GSM3589687 RNA-seq_Dis_07
- GSM3589688 RNA-seq_Dis_08
- GSE289743 Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-Seq FFPE] 83 samples shares anti-pd-1, therapy
- GSE202069 RNA-seq data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients with anti-PD-1 therapy 66 samples shares anti-pd-1, therapy
- GSE303456 Sequential Imatinib and Anti-PD-1 Therapy in KIT-Altered Melanoma: Mechanistic Insights and Clinical Benefit 48 samples shares anti-pd-1, therapy
- GSE272734 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 2] 40 samples shares anti-pd-1, therapy
- GSE78220 mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy 28 samples shares anti-pd-1, therapy
- GSE316970 CYD-4-61 Suppresses Gastric Tumor Growth by Targeting SOX9–CDK4–Driven Oncogenic Programs and Enhances Anti-PD-1 Therapy 18 samples shares anti-pd-1, therapy
- GSE284162 Efficacy of Neoadjuvant Chemotherapy Combined with Anti-PD-1 Monoclonal Antibody in Locally Advanced Resectable Oral Squamous Cell Carcinoma: A Single-Arm Phase II Clinical Trial 12 samples shares anti-pd-1, therapy
- GSE272993 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 1] 360 samples shares anti-pd-1, therapy
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.