A Novel Humanized Immune Stroma PDX Model for Therapeutic Studies
RNA-seq (gene expression) · human · 36 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
- 36 samples: 5 conditions, mostly with about 5 replicates eachGroups 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.
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 GSE222774_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 PRJNA923347 and SRA study SRP417238. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 31 samples.
How we read this: 5 replicated groups read from 36 sample titles; they account for 31 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.
- GSM6932052 Primary Pt. 1 tumor
- GSM6932053 Patient 1 PDX 1 Patient 1 PDX
- GSM6932054 Patient 1 PDX 2 Patient 1 PDX
- GSM6932055 Patient 1 PDX 3 Patient 1 PDX
- GSM6932056 Patient 1 PDX 4 Patient 1 PDX
- GSM6932057 Patient 1 PDX 5 Patient 1 PDX
- GSM6932058 Patient 1 PDX 6 Patient 1 PDX
- GSM6932059 Patient 1 PDX 7 Patient 1 PDX
- GSM6932060 Patient 1 PDX 8 Patient 1 PDX
- GSM6932061 Patient 1 PDX 9 Patient 1 PDX
- GSM6932062 Primary Pt. 2 ascites
- GSM6932063 Patient 2 PDX 1 Patient 2 PDX
- GSM6932064 Patient 2 PDX 2 Patient 2 PDX
- GSM6932065 Patient 2 PDX 3 Patient 2 PDX
- GSM6932066 Patient 2 PDX 4 Patient 2 PDX
- GSM6932067 Patient 2 PDX 5 Patient 2 PDX
- GSM6932068 Patient 2 PDX 6 Patient 2 PDX
- GSM6932069 Patient 2 PDX 7 Patient 2 PDX
- GSM6932070 Patient 2 PDX 8 Patient 2 PDX
- GSM6932071 Primary Pt. 3 ascites
- GSM6932072 Patient 3 PDX 1 Patient 3 PDX
- GSM6932073 Patient 3 PDX 2 Patient 3 PDX
- GSM6932074 Patient 3 PDX 3 Patient 3 PDX
- GSM6932075 Patient 3 PDX 4 Patient 3 PDX
- GSM6932076 Patient 3 PDX 5 Patient 3 PDX
- GSM6932077 Patient 4 PDX 1 Patient 4 PDX
- GSM6932078 Patient 4 PDX 2 Patient 4 PDX
- GSM6932079 Patient 4 PDX 3 Patient 4 PDX
- GSM6932080 Patient 4 PDX 4 Patient 4 PDX
- GSM6932081 Patient 4 PDX 5 Patient 4 PDX
- GSM6932082 Primary Pt. 4 tumor
- GSM6932083 Primary Pt. 5 tumor
- GSM6932084 Patient 5 PDX 1 Patient 5 PDX
- GSM6932085 Patient 5 PDX 2 Patient 5 PDX
- GSM6932086 Patient 5 PDX 3 Patient 5 PDX
- GSM6932087 Patient 5 PDX 4 Patient 5 PDX
- GSE247690 Cellular adaptation to cancer therapy along a resistance continuum [scRNA-seq: PDX] 17 samples shares pdx
- GSE301872 Therapy-persistent leukemia is selectively vulnerable to SLC23A1 restoration via targeting KHSRP (PDX samples from different disease statuses) 15 samples shares pdx
- 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
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares therapeutic
- GSE317680 Single Cell and Spatial Transcriptomics Identify Novel Immune-Stromal Interactions in Cardiac Allograft Vasculopathy 13 samples shares stroma
- GSE294016 A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [bulk RNA-seq] 95 samples shares therapeutic
- GSE290805 Meningioma microenvironment harbors a rich immune landscape with therapeutic implications (Bulk RNA-seq part) 47 samples shares therapeutic
- GSE199939 Comprehensive transcriptomic analysis of immune-related genes in diabetic foot ulcers: New insights into mechanisms and therapeutic targets 21 samples shares therapeutic
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.