GEO series

Gene expression differences between TILs that are reactive to tumor cells and TILs that are not reactive

GSE252437 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/06/30 Platform GPL16791

At a glance

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)
Topic: Breast cancerThis series is part of our curated briefing on it.
Samples: 14 samples: 14 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.

Summary (written by the submitters)

Clinical significance of tumor-infiltrating lymphocytes (TILs) was demonstrated in many tumor types. In the clinical trials, immune check point inhibitors showed significant clinical efficacy in some tumor types with high mutation burden such as melanoma, bladder cancer, and smoking-induced lung cancer, while there were little effects in cancers with lower mutation rates such as breast cancer.

Read the full summary ↓

Recently, selection and adoptive transfer of autologous mutation-specific TILs showed successful regression of metastatic tumors in an estrogen receptor-positive breast cancer patient. In this study, we analyzed gene expression profiles in cultured TILs that are reactive or non reactive against autologous breast cancer cells. We cultured TILs and cancer cells derived from breast tumor tissues obtained from the surgery. Reactivity of TILs against cancer cells was determined by interferon gamma (IFN-γ) ELISA analysis after co-culture of TILs and cancer cells for 24 hours. The total RNA was purified from cultured TILs (post-REP TILs) using RNeasy kits. The gene expression library is generated by Illumina TruSeq RNA library prep kit and sequenced.

This dataset

Open GSE252437 in finder → Find more human RNA-seq datasets → Breast cancer landscape →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE252437_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1060655 and SRA study SRP481082. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 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.

Samples in this study

GSM8001443 BC1544,TIL non response
GSM8001444 BC16043,TIL non response
GSM8001445 BC16092,TIL reaction
GSM8001446 BC16110,TIL reaction
GSM8001447 BC16126,TIL non response
GSM8001448 BC16127,TIL reaction
GSM8001449 BC16147,TIL reaction
GSM8001450 BC16151,TIL non response
GSM8001451 BC16154,TIL reaction
GSM8001452 BC16166,TIL non response
GSM8001453 BC16204,TIL non response
GSM8001454 BC16208,TIL non response
GSM8001455 BC16223,TIL non response
GSM8001456 BC17009,TIL non response

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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.