GEO series

Molecular phenotyping of human endometrium

GSE4888 Homo sapiens (human) Expression microarray 27 samples Submitted 2006/05/24 Platform GPL570

At a glance

Expression microarray · human · 27 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 27 samples: 20 × endometrium vs 6 × endometrium MGroups 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)

To examine the possibility that biochemical or molecular signatures of endometrium may prove to be more useful, we have investigated whole genome molecular phenotyping (54,600 genes/ESTs) of this tissue sampled across the cycle in 28 normo-ovulatory women, using high-density oligonucleotide microarrays.

Read the full summary ↓

The results demonstrate that endometrial samples obtained by two different sampling techniques (biopsy and curetting hysterectomy specimens) from subjects who are as normal as possible in a human study and 4 including those with unknown histology, can be classified by their molecular signatures and correspond to known phases of the menstrual cycle with identical results using two independent analytical methods. Also, the results enable global identification of biological processes and molecular mechanisms that occur dynamically in the endometrium in the changing steroid hormone milieu across the menstrual cycle in normo-ovulatory women. The results underscore the potential of gene expression profiling for developing molecular diagnostics of endometrial normalcy and abnormalities and identifying molecular targets for therapeutic purposes in endometrial disorders. Keywords: Gene expression arrays human endometrium

This dataset

Open GSE4888 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 (GSE4888_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 PRJNA156795. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 16306079) ↗

Study design

20 × endometrium vs 6 × endometrium M

Supports a between-group comparison across 26 samples.

How we read this: 2 replicated groups read from 27 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

GSM109814 endometrium 598 endometrium
GSM109815 endometrium M165 endometrium M
GSM109816 endometrium M169 endometrium M
GSM109817 endometrium M182 endometrium M
GSM109818 endometrium 421 endometrium
GSM109819 endometrium 642 endometrium
GSM109820 endometrium 629 endometrium
GSM109821 endometrium 650 endometrium
GSM109822 endometrium 664 endometrium
GSM109823 endometrium 389 endometrium
GSM109824 endometrium 610 endometrium
GSM109825 endometrium 617 endometrium
GSM109826 endometrium 626 endometrium
GSM109827 endometrium 659 endometrium
GSM109828 endometrium G98A
GSM109829 endometrium M153 endometrium M
GSM109830 endometrium M158 endometrium M
GSM109831 endometrium M163 endometrium M
GSM109832 endometrium 494 endometrium
GSM109833 endometrium 648 endometrium
GSM109834 endometrium 442 endometrium
GSM109835 endometrium 449 endometrium
GSM109836 endometrium 462 endometrium
GSM109837 endometrium 576 endometrium
GSM109838 endometrium 614 endometrium
GSM109839 endometrium 619 endometrium
GSM109840 endometrium 407 endometrium

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GSE94723 Hormone-responsive organoid cultures of human endometrium 9 samples shares endometrium
GSE111976 Single cell RNA-seq analysis on human endometrium across the natural menstrual cycle 2158 samples shares endometrium
GSE6364 Gene Profiling of Endometrium Reveals Progesterone Resistance and Candidate Genetic Loci in Women with Endometriosis 37 samples shares endometrium
GSE310878 Molecular phenotyping of diverse human skeletal muscles with CAGE-Seq 228 samples shares phenotyping
GSE103465 Characterization of gene expression profile during the implantation phase in IVF cycles in endometrium of women with recurrent implantation failure 6 samples shares endometrium

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