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Robust enumeration of cell subsets from tissue expression profiles (HGU133Plus2)

GSE65135 Homo sapiens (human) Expression microarray 28 samples Submitted 2015/03/29 Platform GPL570
At a glance

Expression microarray · human · 28 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Homo sapiens (human)
Samples
28 samples: 14 × FL lymph node biopsy, untreated, vs 5 × Normal tonsil B cells, vs 5 × Normal tonsil T cells, vs 2 × PBMCs, post-RCHOP,Groups 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)
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen, and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content, and closely related cell types. CIBERSORT should enable large-scale analysis of RNA specimens for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu).
This dataset
Open GSE65135 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 (GSE65135_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 PRJNA273241. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25822800) ↗
Study design
14 × FL lymph node biopsy, untreated, vs 5 × Normal tonsil B cells, vs 5 × Normal tonsil T cells, vs 2 × PBMCs, post-RCHOP,

Supports a between-group comparison across 26 samples.

How we read this: 4 replicated groups read from 28 sample titles; they account for 26 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
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