Cellxgene - AdultLungElo - spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

[Wkt8]

Collection/dataset this task is for:

• Title: AdultLungElo - A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche#236
• Project Short Name: AdultLungElo
• ticket link to DCP wrangling ticket https://app.zenhub.com/workspaces/dataset-wrangling-status-5f994cb88e0805001759d2e9/issues/ebi-ait/hca-ebi-wrangler-central/236
• link to ingest UI: https://contribute.data.humancellatlas.org/projects/detail?uuid=957261f7-2bd6-4358-a6ed-24ee080d5cfc&tab=upload
• link to collection in cellxgene:

Relevant People

• Wrangler: Wei Kheng Teh
• Contributor: Elo Maddisoon, Amanda Oliver

Associated files

• SOP
• Knowledge Sharing Drive
• Ingest-cellxgene-submitter
• Cellxgene-schema
• Cellxgene-schema-validate
• Cellxgene-submit-collection

Published study links

• Paper:

• Accessioned data:

Key Events

• [ ] Communicated with contributors and collected necessary files
• [ ] Checked that metadata in the HCA DCP matches up to number of samples in the contributor file
• [ ] Edited and created a final H5ad object
• [ ] Run cellxgene-schema validate
• [ ] Submitted to collection in cellxgene
• [ ] Sent to CellXGene curators (Jason Hilton) to validate
• [ ] Sent to contributors to confirm that publishing will be allowed
• [ ] Collection has been published

[Wkt8]

Meeting with Amanda today to discuss next steps - some analysis files in the HCA need to be updated (See here: https://docs.google.com/document/d/1a5rjrLw3Al2EEWAqewkV-aZbmge0qERR0vQSd2i_VvY/edit)

[Wkt8]

In review with Jason.

[Wkt8]

Jason requested us to get the non-cloupe files for the Visium data and to wrangle the Visium data to cellxgene.