Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: PDX]
Single-cell RNA-seq · human · 17 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 17 samples: 17 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
- Cellular adaptation to cancer therapy along a resistance continuumNature · 2024
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 GSE247690_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1040177 and SRA study SRP471765. 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 17 sample titles: 17 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.
- GSM7898938 vehicle_V1, replicate 1, scRNA-seq
- GSM7898939 vehicle_V2, replicate 2, scRNA-seq
- GSM7898940 resistant_R1-1,replicate 1, scRNA-Seq
- GSM7898941 resistant_R1-2,replicate 2, scRNA-Seq
- GSM7898942 resistant_R3-V,replicate 1, scRNA-Seq
- GSM7898943 resistant_R3-1,replicate 1, scRNA-Seq
- GSM7898944 resistant_R3-2,replicate 2, scRNA-Seq
- GSM7898945 vehicle_V1_per, replicate 1, scRNA-seq
- GSM7898946 vehicle_V2_per, replicate 2, scRNA-seq
- GSM7898947 persister_D1-1, replicate 1, scRNA-seq
- GSM7898948 persister_D1-2, replicate 2, scRNA-seq
- GSM7898949 persister_D2-1, replicate 1, scRNA-seq
- GSM7898950 persister_D2-2, replicate 2, scRNA-seq
- GSM7898951 persister_D3-1, replicate 1, scRNA-seq
- GSM7898952 persister_D3-2, replicate 2, scRNA-seq
- GSM7898953 persister_D4-1, replicate 1, scRNA-seq
- GSM7898954 persister_D4-2, replicate 2, scRNA-seq
- GSE247691 Cellular adaptation to cancer therapy along a resistance continuum 93 samples shares adaptation, resistance, continuum, cellular, therapy, along
- GSE298139 Therapy-resistance in AT/RT is driven by epithelial-mesenchymal transition, extracellular matrix changes, and enrichment of CD1A+ CD207+ dendritic cells [snRNA-seq] 16 samples shares resistance, cellular, therapy
- GSE235863 T cell populations correlate with response and resistance to anti-PD-1 plus lenvatinib combination therapy in hepatocellular carcinoma 69 samples shares resistance, cellular, therapy
- GSE301872 Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (PDX samples from different disease statuses) 15 samples shares pdx, therapy
- GSE271134 Molecular Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Response Prediction in Pediatric AML [pAML PDX Bulk RNA-seq] 14 samples shares pdx, therapy
- GSE311827 AP-1 Mediates Cellular Adaptation and Memory Formation [Bulk RNA-seq] 192 samples shares adaptation, cellular
- GSE234181 Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq] 184 samples shares adaptation, scrna-seq
- GSE273829 GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq] 92 samples shares resistance, 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.