GEO series

Primary human leukocyte RNA expression of unrelated Dutch and UK individuals

GSE20332 Homo sapiens (human) Expression microarray 229 samples Submitted 2010/02/28 Platform GPL6104

At a glance

Expression microarray · human · 229 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 229 samples: 229 × Peripheral blood RNA from sampleGroups 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)

Multiple common variants for celiac disease influencing immune gene expression The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes. We obtained peripheral blood RNA from unrelated Dutch and UK individuals using PAXgene tubes. We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls.

Read the full summary ↓

We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression. *** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***

This dataset

Open GSE20332 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 (GSE20332_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 PRJNA125399. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20190752) ↗

Study design

229 × Peripheral blood RNA from sample

Supports a between-group comparison across 229 samples.

How we read this: 1 replicated groups read from 229 sample titles; they account for 229 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

GSM509318 Peripheral blood RNA from sample 1 Peripheral blood RNA fr…
GSM509319 Peripheral blood RNA from sample 2 Peripheral blood RNA fr…
GSM509320 Peripheral blood RNA from sample 3 Peripheral blood RNA fr…
GSM509321 Peripheral blood RNA from sample 4 Peripheral blood RNA fr…
GSM509322 Peripheral blood RNA from sample 5 Peripheral blood RNA fr…
GSM509323 Peripheral blood RNA from sample 6 Peripheral blood RNA fr…
GSM509324 Peripheral blood RNA from sample 7 Peripheral blood RNA fr…
GSM509325 Peripheral blood RNA from sample 8 Peripheral blood RNA fr…
GSM509326 Peripheral blood RNA from sample 9 Peripheral blood RNA fr…
GSM509327 Peripheral blood RNA from sample 10 Peripheral blood RNA fr…
GSM509328 Peripheral blood RNA from sample 11 Peripheral blood RNA fr…
GSM509329 Peripheral blood RNA from sample 12 Peripheral blood RNA fr…
GSM509330 Peripheral blood RNA from sample 13 Peripheral blood RNA fr…
GSM509331 Peripheral blood RNA from sample 14 Peripheral blood RNA fr…
GSM509332 Peripheral blood RNA from sample 15 Peripheral blood RNA fr…
GSM509333 Peripheral blood RNA from sample 16 Peripheral blood RNA fr…
GSM509334 Peripheral blood RNA from sample 17 Peripheral blood RNA fr…
GSM509335 Peripheral blood RNA from sample 18 Peripheral blood RNA fr…
GSM509336 Peripheral blood RNA from sample 19 Peripheral blood RNA fr…
GSM509337 Peripheral blood RNA from sample 20 Peripheral blood RNA fr…
GSM509338 Peripheral blood RNA from sample 21 Peripheral blood RNA fr…
GSM509339 Peripheral blood RNA from sample 22 Peripheral blood RNA fr…
GSM509340 Peripheral blood RNA from sample 23 Peripheral blood RNA fr…
GSM509341 Peripheral blood RNA from sample 24 Peripheral blood RNA fr…
GSM509342 Peripheral blood RNA from sample 25 Peripheral blood RNA fr…
GSM509343 Peripheral blood RNA from sample 26 Peripheral blood RNA fr…
GSM509344 Peripheral blood RNA from sample 27 Peripheral blood RNA fr…
GSM509345 Peripheral blood RNA from sample 28 Peripheral blood RNA fr…
GSM509346 Peripheral blood RNA from sample 29 Peripheral blood RNA fr…
GSM509347 Peripheral blood RNA from sample 30 Peripheral blood RNA fr…
GSM509348 Peripheral blood RNA from sample 31 Peripheral blood RNA fr…
GSM509349 Peripheral blood RNA from sample 32 Peripheral blood RNA fr…
GSM509350 Peripheral blood RNA from sample 33 Peripheral blood RNA fr…
GSM509351 Peripheral blood RNA from sample 34 Peripheral blood RNA fr…
GSM509352 Peripheral blood RNA from sample 35 Peripheral blood RNA fr…
GSM509353 Peripheral blood RNA from sample 36 Peripheral blood RNA fr…
GSM509354 Peripheral blood RNA from sample 37 Peripheral blood RNA fr…
GSM509355 Peripheral blood RNA from sample 38 Peripheral blood RNA fr…
GSM509356 Peripheral blood RNA from sample 39 Peripheral blood RNA fr…
GSM509357 Peripheral blood RNA from sample 40 Peripheral blood RNA fr…

+ 189 more — browse all 229 samples with per-sample file links →

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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.