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Bulk RNA-seq upload

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For questions contact:

Joe Receveur: jreceveur@som.umaryland.edu

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Files to prepare for uploading

  • Files needed:
      • Metadata +3 tab files (expression.tab,observations.tab,genes.tab)
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Metadata

  • Click ”Gene Expression” from the dropdown window under your account
  • Download metadata template
  • Choose ‘Expression Data’ under Dataset uploader

or

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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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expression.tab

observations.tab

genes.tab

Example (3-tab) Expression Files (RNAseq)

for illustrative purposes

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Ensembl_ID

D0.A

D0.B

D7.A

D7.B

ENSG00000121410

8.237180

3.856151

11.245985

0.0

ENSG00000156006

8.511809

3.699162

11.228691

0.0

ENSG00000196839

8.334226

4.174881

11.159430

0.0

observations

day

replicate

D0.A

0

A

D0.B

0

B

D7.A

7

A

D7.B

7

B

Ensembl_ID

gene_symbol

ENSG00000121410

A1BG

ENSG00000156006

NAT2

ENSG00000196839

ADA

  • This format is easier to programmatically generate, and scales better than Excel spreadsheets.
  • See Wiki for code to convert common inputs into this format
  • 3 tab files need to be zipped into one folder (*.tar.gz)

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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.