HRA000342 - IgANephropathySTRT

[idazucchi]

Project short name:

IgANephropathySTRT

Primary Wrangler:

Arsenios Chatzigeorgiou @arschat

Secondary Wrangler:

Associated files

• Google Drive: folder

Published study links

• Paper: Included data Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy

• Accessioned data: managed access data HRA000342

  • analysis files available from drive

• Ingest

Key Events

• [x] Convert published metadata to HCA spreadsheet
• [x] Manually curate dataset to meet HCA metadata standard
• [x] Collect any matrix and cell-type annotation files
• [x] Upload sheet to validate metadata
• [x] Transfer raw files to ingest to validate data files
• [x] Check linking using ingest graph validator
• [x] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Submit dataset to Production
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch witht the authors to request it

[arschat]

Notes:

Donor

• disease nephrapostasis is not available in ontology and not widely used in medicine. -> closest description I could find in MONDO ontology is nephritis

Cell suspension

• There should be 4 different cell types from enrichment protocol (glomerulus/CD14+/CD14-EPCAM+/CD14-EPCAM-). Only the post analysis cell types are given. -> author responded
• Renamed cell suspensions from NM_XX_XXX to NMXX_XXX in order to avoid surpassing excel cell character limit (32767) in analysis file cell_suspension reference.
• Added same process to each suspension with same specimen/ dissociation/ enrichment to reduce amount of redundant entities

Library prepapration protocol

• Library prep protocol uses a modified STRT method that is also used in a published in DCP dataset. -> Used that as a reference. DCP and ingest

Analysis files

• All PBMC cell suspensions (with the following specimen IDs) although described in the method and the experimental design as part of the procedure, are not included in the given analysis files nor at the tSNE plot on paper. In paper results, blood cells are only used for comparison with IgAN (volcano plots). -> Proceeding without those biomaterials at all. Spreadsheet draft with those files, is uploaded in drive folder.

  PBM_IgAN_10 PBM_IgAN_12 PBM_IgAN_17 PBM_IgAN_19 PBM_IgAN_20 PBM_NM_01 PBM_NM_02 PBM_NM_03 PBM_NM_04 PBM_NM_05

[arschat]

Submission with error in analysis files, and project tab cannot be deleted. Update: submission was deleted with a delay of ~1h

[arschat]

Contacted authors for more info in the enrichment protocol results (enrichment per cell suspension). Replied with a metadata that contained "Position" of each cell suspension, replied for clarifications and a possible match between enrichment and "Position".

Enrichment protocols

• glomerulus
• CD14+ macrophages
• EPCAM+ epithelium
• negative selected cells

  Position

• Glomerulus
• Interstitial
• Non-glomerulus
• Non-glomerulus-Non-macrophage
• Non-macrophage
• Renal

[arschat]

Authors verified the following matching: Position --> enrichment Glomerulus --> glomerulus Interstitial --> negative selected cells Non-glomerulus --> epithelium Non-glomerulus-Non-macrophage --> epithelium Non-macrophage --> epithelium Renal --> macrophages

Since there is no CL ontology for glomerulus or negative selection I omitted the Selected cell types field for the specific cell suspensions and mentioned in the CS description the type of enrichment.

[arschat]

Added changes and submitted spreadsheet. Hit graph validation at 16:44

[ofanobilbao]

@ESapenaVentura to look if the project is really stuck in graph validating

[ESapenaVentura]

Seems ingest crashed down - Does not seem related to this dataset, though, but it has affected graph validation for this dataset

[ofanobilbao]

Submission needs to be put back to Metadata valid and then graph validation re-triggered. @ESapenaVentura to help on this

[amnonkhen]

@amnonkhen to retrigger GV.

[arschat]

graph valid, ready for sec review

[idazucchi]

Project

• update cell count to 3620

Donor

• there is no MONDO term for Nephroptosis, but there is an HP one —> I would use that one instead

Collection

• if you split the protocols split the description too to make it clearer

Specimen

• fill out the nephrectomy samples as normal disease - they have no disease to filter on like this
• this is a bit tricky to represent but the specimens are split in two - glomerulus + rest of the kidney. I would suggest to represent it as:
  • kidney
  • kidney organ part glomerulus This allows the users to filter for glomerulus, but makes it clear that it's not the only tissue analysed. you can also add a sentence to the collection protocol like "Glomeruli were isolated from the tissue, and the rest of the kidney and the glomeruli were processed separately"

Dissociation

• I would split the enzymatic dissociation used to isolate the glomerulus and the one used to dissociate the rest of the kidney to make the experimental design clearer

Cell suspension

• you can use CL:0002518 kidney epithelial cell for the epithelial cells

Enrichment

• use ; not / for marker separator
• I suggest mouth pipetting for glomerulus_enrichment rather than cell picking since the glomerulus is not a single cell and you can make it one protocol with glomerulus_cell_size_enrichment

Sequencing

• not pair ended

Analysis protocol

• normalized_matrix_generation is this needed? the file contains raw cell counts

Analysis file

• no need to fill in the cell count for files that are not matrices

[arschat]

applied sec review comments, added submission but got the following error in metadata validation * Could not retrieve IRI for data:0006 at .file_core.content_description[0].ontology

[arschat]

metadata valid, pushed graph validation on 12:14

[amnonkhen]

I triggered graph validation. It finished successfully.

[arschat]

It is now exported and import form has been sent.