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Cancer-associated fibroblast driven paracrine IL-6/STAT3 signalling promotes migration and dissemination in invasive lobular carcinoma

GSE276108 Homo sapiens (human) RNA-seq (gene expression) 56 samples Submitted 2024/10/11 Platform GPL30173Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 56 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
56 samples: 15 conditions, mostly with about 4 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.
Summary (written by the submitters)
Invasive Lobular Carcinoma (ILC) is an under-studied yet common subtype of breast cancer. A key feature of ILC tumours, due to their single-file invasive growth pattern, is a high stromal content and in particular, an abundance of cancer-associated fibroblasts (CAFs).
Read the full summary ↓
We identified that IL-6 secreted from primary ILC patient-derived CAFs drives STAT3 activation in ILC cell lines and found that IL6, STAT3, pSTAT3 and subsequent downstream gene expression induced by IL-6 within CAF conditioned media is upregulated in ILC tumours compared to Invasive Ductal Carcinoma tumours, the most common subtype of breast cancer. This dataset contains 3`-mRNAseq data from ILC cell lines (SUM44PE and MDA-MB-134VI) and patient-derived organoids (HCI-013 and HCI-018) stimulated with either recombinant human IL-6 (10 ng/ml) for 24 hours or 1 week or SUM44PE cells stimulated with CAF conditioned media (CAF CM)collected from ED26 primary ILC CAFs (characterised here: doi.org/10.3390/cancers14040904) +/- an IL-6 neutralising antibody. RNA was extracted using Qiagen RNeasy mini-kit and libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015).
This dataset
Open GSE276108 in finder → Find more human RNA-seq datasets →
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 GSE276108_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 PRJNA1154703 and SRA study SRP529739. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
15 conditions, mostly with about 4 replicates each
SUM44PE_CMexpt_ctrl ×4 SUM44PE_IL6expt_ctrl24h ×4 SUM44PE_IL6expt_IL624h ×4 SUM44PE_IL6expt_ctrlweek ×4 SUM44PE_IL6expt_IL6week ×4 MM134_IL6expt_ctrl24h ×4 MM134_IL6expt_IL624h ×4 MM134_IL6expt_ctrlweek ×4 +7 more

Supports a between-group comparison across 56 samples.

How we read this: 15 replicated groups read from 56 sample titles; they account for 56 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.

Samples in this study

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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