NR4a knock-down in HER2 CAR-T cells improves T cell longevity and promotes solid tumor eradication [RNA-Seq]
RNA-seq (gene expression) · human · 14 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
- 14 samples: 3 × cont_pre vs 3 × KO_pre vs 3 × cont vs 3 × KOGroups 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
- NR4A ablation improves mitochondrial fitness for long persistence in human CAR-T cells against solid tumorsJournal for immunotherapy of cancer · 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 GSE241456_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 PRJNA1008189 and SRA study SRP456529. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 12 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.
- GSM7729257 cont_pre_1 cont_pre
- GSM7729258 cont_pre_2 cont_pre
- GSM7729259 cont_pre_3 cont_pre
- GSM7729260 KO_pre_4 KO_pre
- GSM7729261 KO_pre_5 KO_pre
- GSM7729262 KO_pre_6 KO_pre
- GSM7729263 cont_1 cont
- GSM7729264 cont_2 cont
- GSM7729265 cont_3 cont
- GSM7729266 KO_4 KO
- GSM7729267 KO_5 KO
- GSM7729268 KO_6 KO
- GSM8421835 CAR-T_pre_WT
- GSM8421836 CAR-T_pre_KO
- GSE241458 NR4a knock-down in HER2 CAR-T cells improves T cell longevity and promotes solid tumor eradication 16 samples shares car-t, nr4a, her2, eradication, knock-down, longevity, improves, promotes
- GSE252799 Zongertinib (BI01810631), an irreversible HER2 TKI, spares EGFR signaling and improves therapeutic response in preclinical models and patients with HER2-driven cancers 90 samples shares her2, improves
- GSE314992 Expression of the CXCR4 S338X variant improves anti-leukemia efficacy of anti-CD19 CAR-T cells 20 samples shares car-t, improves
- GSE243375 HER2 heterogeneity and treatment response-associated profiles in HER2-positive breast cancer in the NCT02326974 clinical trial 287 samples shares her2
- GSE234519 NSABP B-41: A Study of AC Followed by a Combination of Paclitaxel Plus Trastuzumab or Lapatinib or Both Given Before Surgery to Patients With Operable HER2 Positive Invasive Breast Cancer 245 samples shares her2
- GSE255359 High mechanical conditioning by tumor extracellular matrix stiffness is a predictive biomarker for anti-fibrotic therapy in HER2-negative breast cancer 108 samples shares her2
- GSE274142 Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Patients with HR+/HER2- Metastatic Breast Cancer 89 samples shares her2
- GSE271080 Randomized phase II trial of preoperative fulvestrant with or without enzalutamide for ER+/Her2- primary breast cancer 86 samples shares her2
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.