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Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness

GSE266935 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2024/12/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 13 conditions, mostly in duplicateGroups 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
Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsivenessNPJ breast cancer · 2024
Summary (written by the submitters)
Organoid cultures offer a powerful technology to investigate many different aspects of development, physiology, and pathology of diverse tissues. Unlike standard tissue culture of primary breast epithelial cells, breast organoids preserve the epithelial lineages and architecture of the normal tissue. However, existing organoid culture methods are tedious, difficult to scale, and do not robustly retain estrogen receptor (ER) expression and responsiveness in long-term culture.
Read the full summary ↓
Here, we describe a modified culture method to generate and maintain organoids as suspension cultures. This method improves organoid growth and uniformity over the traditional Matrigel dome embedding method while still maintaining the fidelity of the three major epithelial lineages. Using this adopted method, we are able to isolate and culture hormone sensing (HS) cells alone that retain ER responsiveness upon estrogen stimulation in long-term culture. This culture system presents a valuable opportunity to study the events involved in initiation and evolution of ER-positive breast cancer.
Published in
Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness
Chang KC, Silvestri F, Oliphant MUJ et al. · NPJ breast cancer 2024 · PMID 39702422 · doi:10.1038/s41523-024-00714-7
This dataset
Open GSE266935 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 GSE266935_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 PRJNA1108743 and SRA study SRP506187. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39702422) ↗
Study design
13 conditions, mostly in duplicate
ORG6HS_7dculture ×3 ORG1HS-control ×2 ORG1HS_E21nM ×2 ORG5HS-control ×2 ORG5HS_E21nM ×2 ORG11HS-control ×2 ORG11HS_E21nM ×2 ORG6HS_suspension ×2 +5 more

Supports a between-group comparison across 27 samples.

How we read this: 13 replicated groups read from 27 sample titles; they account for 27 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
Datasets on a similar topic

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