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Project: Submission Spreadsheet

Title: Example Entries



Introduction

The purpose of this document is to detail the requirements for filling out entries in the spreadsheet designed for the submission of Microarray Data to the GUDMAP database.

The GUDMAP Microarray spreadsheet also includes many fields that are additionally required for the submission of data to Gene Expression Omnibus (GEO), a public repository that stores high-throughput experimental data including microarray data. It is anticipated that data submitted to GUDMAP can be easily incorporated into GEO and vice versa.

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GEO Submissions

GEO requires that users supply 3 types of information: Platform, Sample, and Series data.

For more details of GEO submissions, go to the following link:
http://www.ncbi.nlm.nih.gov/projects/geo/info/overview.html


Image taken from:
http://www.ncbi.nlm.nih.gov/projects/geo/info/overview.html

Microarray data submitted to GUDMAP is automatically submitted to GEO.  The spreadsheet captures data that is required for submission to both the GUDMAP & GEO databases.

Currently, GUDMAP accepts only microarray data from Affymetrix chips.

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GUDMAP Microarray Spreadsheets

The data required for a GUDMAP Microarray submission is organised into one Excel workbook.

The workbook contains 2 spreadsheets.
a. Sheet 1 - The Sample Data Sheet (incorporating sample, platform data & supplementary Affymetrix files associated with each sample eg. CEL, CHP, EXP, RPT, TXT files)
b. Sheet 2 - The Series Data Sheet (series data only)

IMPORTANT:  Only alpha-numeric characters (A-Z, 0-9) will be accepted in both the image directory and the image filenames.  The only exception to this is an underscore [ _ ] and the dot [ . ] before the file extension.

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GUDMAP Sample Data (Sheet 1)
Sample data describes the biological material examined and the measurements derived from analysis of this material.

Unique ID / Sample Name (Column 0)
Enter here a unique ID for each row. This can be any unique value but labs may wish to use an ID that they hold locally. Only alpha-numeric characters (A-Z, 0-9) will be accepted for a Unique ID.  The only exception to this is an underscore [ _ ] used instead of a space e.g. Tie2_Glom1, CRYM_P1.

Associated File (Column 1)

Leave this column blank. This is not a required field.

 

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Submitter / PI Details (Columns 2-9 & 10-17)
Enter here the contact details of both the submitter and the principal investigator.  Details include name, address, email and telephone number.


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Sample Name & Specimen Details (Columns 18-27)
Enter the sample name again in column 18. For specimen details, one should pay particular attention to the following columns;

Tissue / Cell Type (Column 19)

Enter here the anatomical component(s) from which the RNA was isolated e.g. Adult ureter, E15.5 early proximal tubule.

Ontology Name (Column 20)
Enter here the anatomical component from which the RNA was isolated e.g. ureter, early proximal tubule.  The Editorial Office will change this to the EMAP ID of the anatomical component(s) sampled, a requirement for the GUDMAP submissions process.

Mutations (Column 24)
Copy here the details from ‘Transgenic Allele Name (Column 66)’ or from ‘Local Allele ID (Column 72)’ if transgenic reporter or mutant mice strains are used in the experiment. These column details facilitate the uploading of further transgenic reporter allele (Columns 65-69) and mutant allele details (Columns 70-79) respectively to GUDMAP.

Sex (Column 27)
Options include ‘male’, ‘female’, ‘unknown’, or ‘both'.


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Staging & Dissection Method (Columns 28-33)

Enter the staging details and dissection method. For more details on staging, go to the following link:

http://www.gudmap.org/About/Tutorial/DevMUS.html#Staging

Developmental Stage (Columns 28)
Enter here the developmental stage of the specimen sampled.

Theiler Stage (Columns 29)
The Editorial Office will add the Theiler Stage.

Dissection Method (Column 32)
Enter a brief description of the method used to dissect the component under study e.g. Laser capture micro-dissection; Collagenase treatment, differential sieving, trypsinization & fluorescent activated cell sorting; Whole organ excision.

Sample Image (Column 33)
An image illustrating the source of the sample should be provided. This image could show the target structure before and following laser capture or FACS vs control cell plots. Enter the filename of the image in Column 33 and use the vertical slash (pipe) symbol to separate filenames when including multiple images.  Please ensure that the sample image filenames in the spreadsheet match the filenames of the sample images by using the copy and paste functions.

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RNA Quality (Columns 34-36)
Enter here details relating to the quality of the RNA.
 
In Column 35 we would like the A260/280 index i.e. the ratio of UV absorbance readings at 260 nm and 280 nm giving a general assessment of RNA quality (with 1.8 - 2.0 being ideal).

In Column 36 we would like the Bioanalyzer RIN i.e. the RNA Integrity Number provided by Agilent's Bioanalyzer. Again this is a general assessment of RNA quality (with 10 being highest quality and 1 being lowest).

 


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Platform Details (Columns 37-41)
Enter here details of both the array name, design and manufacturer protocols.



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RNA Extraction & Target Amplification Protocols (Columns 42–47)

Target Amplification Manufacturer Kit (Column 43)

Enter here the name of the kit used to amplify the RNA e.g. TargetAmpTM 2-Round Aminoallyl -aRNA AmplificationKit 1.0 (EPICENTRE iotechnologies), WT-OvationTM Pico RNA Amplification System (NuGEN).

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Hybridization Protocols & Analysis (Columns 48-51)

In Column 48 describe the array hybridization & wash protocols.
In Columns 49 to 50 describe data analysis protocols.
In Column 51, enter details relating to the standard RNA reference that was used for the purpose of comparing multiple experiments e.g. P0.5 whole embryo RNA.

Experimental Goals and Design (Columns 52-53)
In Columns 52 and 53, describe the experimental goals and experimental design, respectively.

 


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GUDMAP Associated Files (Columns 54-58)
Enter the filenames of the associated Affymetrix files. Please ensure the filename extension is in upper case.

CEL (Column 54)

The Cell Intensity file (.CEL) contains fluorescence intensities for each probe on the microarray.  Enter here the name of the associated CEL file for this ID.

CHP (Column 55)

The Chip file (.CHP) contains signal values and presence / absence calls for each probe set on the microarray.  Enter here the name of the associated CHP file for this ID.

RPT (Column 56)

The Report file (.RPT) includes information about noise and internal hybridisation controls within the chip.  Enter here the name of the associated RPT file for this ID.

EXP (Column 57)

The Experiment Information file (.EXP) includes information relating to the hybridisation protocol.  Enter here the name of the associated EXP file for this ID.

TXT (Column 58)

The Expression Analysis file (.TXT) is a text version of the .CHP file.  It contains this information in a tab-delimited format.  Enter here the name of the associated TXT file for this ID.

IMPORTANT:  Only alpha-numeric characters (A-Z, 0-9) will be accepted in both the associated filenames.  The only exception to this is an underscore [ _ ] instead of spaces and the dot [ . ] before the file extension.

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Sample Label & Scan Protocols (Columns 63 & 64)
Enter the kit used to Label the RNA in Column 63 e.g.  Biotin-X-X-NHS (EPICENTRE Biotechnologies), FL-Ovation cDNA Biotin Module V2 (NuGEN).  

Add the Affymetrix scan protocol in to Column 64 e.g. Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix scanning software Genechip Operating Software Version 1.4.

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Transgenic Reporter Details (Columns 65-69)
Columns are provided to allow the submitter to document details of the transgenic reporter allele(s), if applicable.


Transgenic Allele ID (Column 65)
Enter the database ID for the transgenic reporter e.g. MGI or MMRRC ID.(MMRRC:011834-UCD).


Transgenic Allele Name (Column 66)
Enter the allele name as specified in the database e.g. Tg(Mafb-EGFP)79Gsat. 


Transgenic Reporter (Column 67)
Enter the type of reporter e.g. GFP, EGFP, RFP, lacZ, luciferase.


Transgenic Visualisation (Column 68)
Enter here the visualisation methods used to detect the reporter e.g. anti-GFP Ab, transgene fluorescence, B-gal+Xgal, luciferase+luciferin.


Transgenic Reporter Notes (Column 69)

Enter here any additional notes the author would like users to be made aware of concerning the transgenic reporter.  This could even be a PMID Publication.

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Mutant Allele Details (Columns 70-79)
Columns are provided to allow the submitter to document details of the mutant allele(s), if applicable.

Mutated Gene ID (Column 70)
Enter the database ID for the gene symbol e.g. MGI (MGI:98912).

Mutated Gene Symbol (Column 71)
Enter the MGI-recognised gene symbol e.g. Upk1b.

Local Allele ID (Column 72)
Enter the database ID for the mutant allele e.g. MGI:4441453.

Local Allele Description  (Column 73)
Enter the allele description e.g. targeted knock in or targeted knock out.

Allele on First Chromatid (Column 74)
Enter the Allele Name as described in the database.  Please note MGI automatically updates the names of targeted mutation so that they include the up-to-date name of the Gene symbol e.g. Upk1btm1Zhang

Allele on Second Chromatid (Column 75)

Enter the allele name specified in the database.  Please note MGI automatically updates the names of targeted mutation so that they include the up-to-date name of the Gene symbol.  If this specimen is a heterozygote, leave this field blank.

Non-paired or Missing -Chromosome (Column 76)
This should be used in instances of mutations on the sex chromosomes or alternatively in instances where a mutation localises to a site of translocation etc.

Reporter (Column 77)
Enter the type of reporter e.g. GFP, EGFP, RFP.

Visualisation (Column 78)
Enter here the visualisation methods used to detect the reporter e.g. anti-GFP Ab, transgene fluorescence, B-gal+Xgal, luciferase+luciferin.

Notes (Column 79)
Enter here any additional notes the author would like users to be made aware of concerning the mutant allele.

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GUDMAP Series Data (Sheet 2)


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

For more info on series data, go to the following link:
http://www.ncbi.nlm.nih.gov/projects/geo/info/depguide.html#SubmitSeries

Standard Fields Table

The Standard Fields Table contains information relating to the design of the experiment and requires both a title and a summary.


For a GUDMAP Microarray submission, we require submitters to complete three additional fields not found in GEO. These are listed below:

Sample ID Table
The Sample ID Table should contain the unique ID from the Sample Data Sheet (in Column A) along with a description of that sample (in Column B).


Variable Table
The Variable Table follows GEOarchive metadata guidelines (http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html#GAmeta).

The variable (Column A) is a required field. Variables can be one of the following: dose, time, tissue, strain, gender, cell line, development stage, age, agent, cell type, infection, isolate, metabolism, shock, stress, temperature, specimen, disease state, protocol, growth protocol, genotype/variation, species, individual, or other.

A description (Column B) is additionally a required field. Descriptions should include information about the developmental stage and tissue from which RNA was extracted.

In Column C, unique IDs relating to individual samples should be entered. Multiple IDs are to be pipe (I) separated. Please note that unique IDs should only appear once in the variable table - GEO will not accept IDs that appear in multiple rows of the variable table.

Replicates Table
The Replicates Table follows GEOarchive metadata guidelines (http://www.ncbi.nlm.nih.gov/projects/geo/info/spreadsheet.html#GAmeta).

There are three options for the replicate type (Column A). These are: 1) biological replicate; 2) technical replicate - extract; 3) technical replicate - labeled-extract. Enter one of these terms into Column A.

In Column B, unique IDs relating to individual samples should be entered. Multiple IDs are to be pipe (I) separated.

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