Single Cell RNA-seq upload via Excel

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For questions contact:

Joe Receveur: jreceveur@som.umaryland.edu

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Files for uploading

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• Metadata+ formatted Excel sheets (expression,observations,genes)
• Counts must be normalized!
• Any common normalization method is accepted
• If you need assistance with normalization, contact the curator team

Metadata

• Click ”Gene Expression” from the dropdown window under your account

• Download metadata template

• Choose ‘Expression Data’ under Dataset uploader

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Example Metadata

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Must be numeric value

GSE number must be publicly available, otherwise, leave it blank

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Verify Metadata

Choose upload file to upload your completed metadata template

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Any fields with issues will highlight red and the message column describes what is wrong.

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Scroll to the bottom and click Continue

Taxonomy ID is missing: 10090

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Example Expression File - Excel format

hESC (H9) in vitro neural differentiation timecourse (CORTECON; van de Leemput et al. 2014, Neuron)

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The expression tab must be keyed on Ensembl ID. The other columns are expression values per cell/tissue, data must be normalized (fpkm, rpm, etc

The genes tab is where you can add annotations for each gene.

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Example Expression File - Excel format

hESC (H9) in vitro neural differentiation timecourse (CORTECON; van de Leemput et al. 2014, Neuron)

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• The observations tab is where you can add details for each cell/condition column.

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• gEAR accepts all your annotations.‘replicate’ is useful for comparison tool.

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• If you don’t have any replicate, please do not include that column, otherwise, cause errors

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expression.tab

observations.tab

genes.tab

Example (3-tab) Expression Files (scRNAseq)

for illustrative purposes

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• This tag is necessary for using comparison tool I if you have replicates

• This tag is necessary to use primary analysis in sc workbench

Limit the length for less than 15 characters

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Upload Expression

data

All of the following are links to example files for you to view in each accepted format:

upload the excel/(3 tab zip files) using this link:

It will automatically load and validate the file.

Upload help

• Our curation team is happy to help with any issues related to gEAR:

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• Formatting data for upload
• Upload
• Curation and profile assistance

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• The curation team is independent from ear researchers involved in the gEAR platform

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To reach us for assistance:

• Contact button on homepage
• Direct email: jreceveur@som.umaryland.edu