GUDMAP1/GUDMAP2/nGUDMAP: Quality Control - ISH (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 quality control used by the Editorial Office in the University of Edinburgh for ISH data in GUDMAP1, GUDMAP2 and nGUDMAP.

Procedure

Aim

To check the quality of the annotated high-resolution renal ISH data in GUDMAP against data in peer-reviewed, published literature.

Method

1. For each gene ‘xxx’ in the annotated, high resolution, ISH entries in GUDMAP, search PUBMED for xxxx kidney.
2. Manually select abstracts that look as if they have ISH data in them.
3. Filter these for coincidence (or near-coincidence) with the stage(s) in GUDMAP.
4. View the ISH in the papers and read the text and score for agreement or disagreement with GUDMAP. Note when published text is wrong with respect to published figures (this sometimes happens when a paper is really about other organs and mentions kidney in passing: it is common for any tube-like things to be called a ‘glomerulus’).

Results

There were 78 genes that appeared in both high-resolution GUDMAP ISH and Pubmed ISH: of these, 14 had entries in both GUDMAP and publications that covered the same developmental stage. 71% agreed completely, 14% showed partial agreement with no actual disagreement (this means that the paper and GUDMAP studied sets of renal structures that overlap only partially; for example the ureter was visible in only one data set and annotation). 14% showed disagreement in text but not in the images: in each case the GUDMAP annotation was correct and the other obviously wrong.

Consortium

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium