GEO series

Prospective derivation of a 'Living Organoid Biobank' of colorectal cancer patients

GSE64392 Homo sapiens (human) Expression microarray 37 samples Submitted 2015/05/07 Platform GPL16686

At a glance

Expression microarray · human · 37 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 37 samples: 37 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 expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

In Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. We report the establishment of tumor organoid cultures from 20 consecutive colorectal (CRC) patients. For most, organoids were also generated from adjacent normal tissue. The organoids closely resemble the original tumor.

Read the full summary ↓

The spectrum of genetic changes observed within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. Gene expression analysis indicates that the major CRC molecular subtypes are represented. Tumor organoids are amenable to robotized, high-throughput drug screens allowing detection of gene-drug associations. As an example, a single organoid culture was exquisitely sensitive to Wnt secretion (porcupine) inhibitors and carried a mutation in the negative Wnt feedback regulator RNF43 (rather than in APC). Organoid technology may fill the gap between cancer genetics and patient trials, complement cell line- and xenograft-based drug studies and allow personalized therapy design.

This dataset

Open GSE64392 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 (GSE64392_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 PRJNA270877. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25957691) ↗

Study design

37 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 37 sample titles: 37 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

GSM1570172 p5n
GSM1570173 p5t
GSM1570174 p6n
GSM1570175 p6t
GSM1570176 p7n
GSM1570177 p7t
GSM1570178 p8n
GSM1570179 p8t
GSM1570180 p9n
GSM1570181 p10n
GSM1570182 p10t
GSM1570183 p11n
GSM1570184 p11t
GSM1570185 p16n
GSM1570186 p16t
GSM1570187 p17t
GSM1570188 p18n
GSM1570189 p18t
GSM1570190 p19ta
GSM1570191 p19tb
GSM1570192 p20n
GSM1570193 p20t
GSM1570194 p23n
GSM1570195 p24n
GSM1570196 p24ta
GSM1570197 p24tb
GSM1570198 p25t
GSM1570199 p26n
GSM1570200 p26t
GSM1570201 p27n
GSM1570202 p27t
GSM1570203 p28n
GSM1570204 p9t
GSM1570205 p14t
GSM1570206 p23t
GSM1570207 p28t
GSM1570208 p31t

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