GUDMAP1/GUDMAP2/nGUDMAP: Manual checking protocols - Microarray Data (Version 1.0)

Version

1.0

Notice

This page is the corresponding protocol tomestone page generated as part of the ATLAS-D2K shutdown in July 2025. Many links on this page may be broken.

Authors

Richard Baldock

Release Date

2017-09-19

Abstract

This protocol describes methods used used by the Editorial Office in the University of Edinburgh for manually checking microarray data in GUDMAP1, GUDMAP2 and nGUDMAP.

Procedure

Manual Checking Protocols

Sheet 1 / Sample Data Sheet incorporates sample & platform data

Unique ID
A Unique Identifier for each submission is given by the submitter.

Person Details
Checks ensure that the Submitter, Authors, submitting lab and PI lab details are correct.

Specimen Details
Tissue cell type, ontology name, genus / species, strain, mutation, pool size, sex, developmental stage and Theiler Stage are checked.  The ontology name is given as an EMAP ID and this needs to correlate with the Theiler Stage.  The developmental stage given by the submitter should match the appropriate Theiler Stage for GUDMAP.

Sample Image
Sample image sent must illustrate the source of the sample eg. laser capture or the quality of the FACS process. 

RNA Quality Details
Details checked.

Platform Details
Checks with the Affymetrix website ensure the accuracy of information given.

Experimental Goals, Experimental Designs and Dissection Method
Checks ensure the accuracy of the information given.

Associated Files
Checks carried out of the details of associated files that support the array submission i.e. CEL, CHP, RPT, EXP and TXT files. This ensures that the correct associated files are uploaded to the entry.

Non_Wildtype Details
Checks carried out using other databases. eg. MMRRC, PUBMED

Transgenic Reporter Alleles
Checks carried out using other databases. eg. MMRRC, PUBMED

Sheet 2 / Series Data Sheet contains the series data

Series data links together groups of samples and describe study as a whole.

Standard Fields Table
Table contains information relating to the design of the experiment and requires both a tile and summary.  Checks ensure the accuracy of information given.

Sample ID Table
Table contains the Unique ID from the Sample Data Sheet along with a description of that sample.  Checks ensure the accuracy of information given.

Variable Table
Table follows the GEO archive metadata guidelines.  Checks ensure the accuracy of information given.

Replicates Table
Table follows the GEO archive metadata guidelines.  Checked ensure the accuracy of information given.

Consortium

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium