GEO series

Expression profiles of cell populations purified from human CRC (3 ways)

GSE39395 Homo sapiens (human) Expression microarray 24 samples Submitted 2013/01/17 Platform GPL570

At a glance

Expression microarray · human · 24 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 24 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy.

Read the full summary ↓

A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease. We purified by FACS [CD45(+),Epcam(-)], [CD45(-) Epcam(+)] and [CD45(-) Epcam(-)] cell populations from fresh CRC samples and assessed their gene expression profiles

This dataset

Open GSE39395 in finder → Find more human 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 (GSE39395_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 PRJNA170773. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23153532) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 24 more — browse all 24 samples with per-sample file links →

Datasets on a similar topic

GSE247998 Brain and Blood Transcriptome Profiles Delineate Common Genetic Pathways across Suicidal Ideation and Suicide 100 samples shares profiles, ways
GSE333925 Gene expression profile of 31 RAS/RAF-wild-type colorectal cancer (CRC) stem-cell (SC) spheroids and 7 FGFR-inhibitor resistant CSC-SC spheroids 38 samples shares crc
GSE256000 Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [RNA-seq] 32 samples shares crc
GSE33000 Gene expression profiles of human prefrontal cortex brain tissues 624 samples shares profiles
GSE294559 Single-cell multi-omics characterize colorectal tumors, adjacent healthy tissue and matched organoids identifying CRC-unique features 72 samples shares crc
GSE302903 Single-cell RNA sequencing of tumor tissues from 12 colorectal cancer (CRC) patients. 12 samples shares crc
GSE221608 Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC 52 samples shares crc
GSE254366 Epigenome reprogramming through H3K27 and H3K4 trimethylation as a resistance mechanism to DNA methylation inhibition in BRAFV600E-mutated CRC. 36 samples shares crc

Search all human microarray datasets in GEO →

Share this dataset

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.