GUDMAP1/GUDMAP2/nGUDMAP: Manual checking protocols - ISH / IHC / Tg 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 in situ data in GUDMAP1, GUDMAP2 and nGUDMAP.
Procedure
Manual Checking Protocols
Submission ID Checks ensure the Unique Identifier for each submission given by the submitter is in the correct format.
Person Details Checks ensure that the Submitter, Authors, submitting lab and PI lab details are correct.
Probe Details Clone name, sequence Accession ID, Gene details & probe additional notes checked using the MGI & NCBI databases.
Specimen Details Stage, strain, sex, genotype, fixation / embedding method and discussion notes checked.
Images Details Checks ensure the filenames are in the accepted format for database entry and that the short note given for each image corresponds to the number of image filenames.
Annotation I & II Columns Checks ensure that the correct format and annotation rules are being followed.
The online annotation tool replaces this part of the spreadsheet. Checks on the submissions annotated using the online annotation tool are carried out to ensure that the sex and Theiler stage given are the same as in the spreadsheet.
Related Data Columns Related Data Database, Related Data Submission ID & Related Data type checks ensure that the submission data is linked to the correct data sets in either GUDMAP or other databases since this additional information can support the interpretation of the results displayed in GUDMAP.
Acknowledgements Submitter acknowledgements are checked to ensure they are correct.
References The publication reference details given in these columns show where the data has been published for further reading and are checked.
Tissue Type Column Checks ensure that the correct tissue has been assayed and matches the annotated data and the sex of the specimen.
Non_Wildtype Details Checks carried out using other databases e.g. MMRRC, PUBMED.
**Transgenic Reporter Alleles ** Checks carried out using other databases e.g. MMRRC, PUBMED.
Results Notes Checks ensure that the correct data note is included e.g. sex-related gene expression difference observed in the gonad.
Further computational checks
The spreadsheet is put through the parser & image checker. Checks ensure that:
- The data is acceptable for uploading to the GUDMAP public database
- The images are all present on the archive site
Errors flagged by the parser are manually checked by the Editor:
- The primer coordinates are determined using the ‘probe checker’ and are added to the spreadsheet. This checks that the primers match the sequence accession ID given in the spreadsheet.
- Any recommended changes are made to the spreadsheet and / or highlighted in an EO report and sent to the submitter for comment.
- Once comments have been received from the submitter the spreadsheet is amended and put through a final parser & image check before sending it to Derek for uploading to the database.
- Once data is public an email is sent to the submitter for further checks. Any issues arising are corrected by the EO.
For more details on automated checking protocols please see the following links:
Consortium
GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium
