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Pre-metastatic expression array day 7

GSE30885 Mus musculus (mouse) Expression microarray 12 samples Submitted 2011/07/25 Platform GPL8321

At a glance

Expression microarray · mouse · 12 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Mus musculus (mouse)
Samples: 12 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow-derived cells. Here we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells in mouse models of breast cancer. Tumor-entrained neutrophils (TENs) inhibit metastatic seeding in the lungs by generating H2O2, and tumor-secreted CCL2 is a critical mediator of optimal anti-metastatic entrainment of G-CSF-stimulated neutrophils.

Read the full summary ↓

TENs are present in the peripheral blood of breast cancer patients prior to surgical resection but not in healthy individuals. Thus, while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site. To follow the earliest transcriptional changes in pre-metastatic tissues, we orthotopically injected 4T1 cells into the mammary fat pad of female nude mice. Control mice were orthotopically injected with PBS. 7 days post tumor engraftment, the mice were sacrificed and thoroughly perfused with ice cold PBS, and lung and liver samples were flash frozen in liquid nitrogen. Following RNA extraction, the lung and liver RNA samples were analyzed on MOE430A2 Affymetrix arrays using R/Bioconductor software.

This dataset

Open GSE30885 in finder → Find more mouse microarray datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE30885_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA154585. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21907922) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

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