E-MTAB-13687 - MassoniBadosaHumanTonsil

[idazucchi]

Project short name:

MassoniBadosaHumanTonsil

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Associated files

• Google Drive: folder

Published study links

• Paper: An atlas of cells in the human tonsil

• Accessioned data: E-MTAB-13687

Ingest - preprint Ingest

Key Events

• [ ] Convert published metadata to HCA spreadsheet
• [ ] Manually curate dataset to meet HCA metadata standard
• [ ] Collect any matrix and cell-type annotation files
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [ ] Upload sheet to validate metadata
• [ ] Transfer raw files to ingest to validate data files
• [ ] Check linking using ingest graph validator
• [ ] 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

[idazucchi]

Imaging

Unclear microscopy setup, no magnification specified

Files

Visium

I'm not sure if we want to keep the html summary files + the metric_summary I'm removing:

• tonsil_atlas_donor_metadata.csv - just donor metadata we already have
• BCLL-names_convert.xlsx and donor_ids.txt - same content, but the ids mentioned are not found elsewhere
• V10M16-059.gpr, V19S23-039.gpr - layout file in gpr format for the slide spots, can be obtained from 10x

[idazucchi]

I've swapped the doi of the pre-print for the publication's one I've created a new project in ingest for the publication, the pre-print is still in ingest as not elegible --> we can revise but we should keep track of the doi since it's an bionetwork paper

[arschat]

Very admirable job, Ida! Huge dataset, with many and complex designs. Excellent work, more power to your elbow!

So, here are my comments.

Project

• Contributors, move middle name initial between commas instead of first name
• Publications, remove space after double pipe
• Funders, although europePMC has 3 funding entries, in the acknowledgements there are multiple grant IDs
  Funding table

Grant ID	Funding Organization
810287	European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
PID2020-115439GB-I00	Ministerio de Ciencia e Innovación (MCI)
PID2020-118167RB-I00	Ministerio de Ciencia e Innovación (MCI)
RTI2018-094274-B-I00	Ministerio de Ciencia e Innovación (MCI)
PI19/01772	Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias, co-funded with ERDF funds
unspecified	Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program
BIO2015-71792-P	MINECO/FEDER, European Regional Development Fund
unspecified	Centro de Excelencia Severo Ochoa and the Generalitat de Catalunya
2021-SGR-1172	Suport Grups de Recerca AGAUR
2021-SGR-1343	Suport Grups de Recerca AGAUR
unspecified	Accelerator award CRUK/AIRC/AECC joint funder-partnership
CB16/12/00225	CIBERONC
CB16/12/00334	CIBERONC
KU1315/14-1	Deutsche Forschungsgemeinschaft (DFG)
HA5354/10-1	Deutsche Forschungsgemeinschaft (DFG)
HA5354/12-1	Deutsche Forschungsgemeinschaft (DFG)
SPP1937 (HA5354/8-2)	Deutsche Forschungsgemeinschaft (DFG)
HA5354/13-1	Deutsche Forschungsgemeinschaft (DFG)
220540/Z/20/A	Wellcome Trust
223092/Z/21/Z	Wellcome Trust Senior Research Fellowship
unspecified	NIHR Newcastle Biomedical Research Centre
unspecified	Lister Institute for Preventative Medicine
BIL KLS-5130-08-2020	Swiss Cancer League
unspecified	Nuovo-Soldati Foundation for Cancer Research
unspecified	Institucio Catalana de Recerca i Estudis Avancats (ICREA) of the Generalitat de Catalunya

Donor organism

• Nice catch adding the two extra donors
• Development stage in AE is not from HsapDv ontology, although similar stage exists like child stage: HsapDv:0000081 and human adult stage: HsapDv:0000087. We usually add the HsapDv ontology field so this would be a decision between consistency among HCA DCP projects or within project across platforms.

Specimen from organism

• PRESERVATION METHOD for the last two specimens it is mentioned

  For the final part of the study, cryopreserved cells from tonsil samples of two MCL patients were used (age 64 and 80, both male). MCL samples were obtained from cryopreserved dissociated cells from tonsils, from the ICGC case collection of Hospital Clinic, Barcelona.

we do not know if the specimen was processed (dissociated) fresh or preserved, but since it was preserved at some point, do you think it is worth adding cryopreservation, other here?

• Nice catch specifying the collection_site in the location field

Imaged specimen

• There seems to be an error with the accession numbers. Although I could find the accessions in ENA, it is different from the one listed in AE. For example, for visium_sample_1:
  • spreadsheet accession
  • ae accession

Same problem exists in the cell_suspension accessions and run accessions as well. I would guess that there was an update on the AE submission, and they updated all the accession because the Sample Alias of ENA adds a "_2" in the AE provided accession.

Enrichment protocol

• markers could be filled based on the Fig 6F plot, I think it should be mono_dend: SLAN+ CD14+ CD16+, slan: SLAN+ CD14- CD16- CD11C- CD123-

Cell suspension

• There are 13 cell suspensions that are not referenced in any file tab (scRNA_Sample_15_hashed, scRNA_Sample_16_hashed, scRNA_Sample_17_hashed, scRNA_Sample_1, scRNA_Sample_2, scRNA_Sample_3, scRNA_Sample_4, scRNA_Sample_5, scRNA_Sample_6, scRNA_Sample_7, scRNA_Sample_11, scRNA_Sample_12, scRNA_Sample_13). Is that on purpose?
  • Problem with accessions, see ### Imaged specimen

Sequencing protocol

• sequencing method text for "ATAC_NextSeq" vs "multiome_snATACseq_sequencing", in the first is assay for transposase-accessible chromatin using sequencing while in the second its single cell assay for transposase-accessible chromatin using sequencing. Although they have the same ontology, this might be misleading that the first is bulk ATAC.

Sequence file

• Read index, for libraries that contain 3 read files (for example MCL.M102.BCLLATLAS_65.kpi1zxjo_542l3n1f.220596.ATAC.P10.R3.fastq.gz) have index1 for R2 files and read2 for R3 files. We have the option to record the read1 up to read4 in our last sequence file schema, while AE might not have this. In the methods for scATAC it is mentioned that there are R1 R2 I1 I2 files instead. We could either stick to the AE and leave it R2 as index1 and R3 read2, or stick to the filenames, and change it R2 to read2 and R3 to read3.
• You could add ArrayExpress as FILE SOURCE
• Similarly with ### Imaged specimen and ### Cell suspension, run accessions are outdated, and have been suspended.

Analysis protocol

• Although the alignment software mentioned for multiome_matrix_generation is Cellranger, the version is stated to be v1.0 which did not offer the GRCh38 version (here). The command stated also, is cellranger-arc which might be a hint that they used Cellranger ARC for multiome ATAC & GEX.

Analysis file

• Awesome! We could add MATRIX CELL COUNT for some files (based on the number of lines in their _barcodes.tsv). For convenience I added the file that could be extracted here MassoniBadosaHumanTonsil_matrix_cell_count.txt

Supplementary file

• all 3 files have only the ontology text field for the content description and id & label is missing (maybe a problem with fill_ontologies script and graph validation?)

[idazucchi]

Verified in the browser Something weird is happening:

1. the donor number displayed in the overview is 17 (wrong) but in the download tab it's 19 (correct)
2. the matrix files for 2 donors are missing from the matrices tab but not from the download tab

In case it helps explain the above: the 2 donors above have no sequence files but do have analysis files Since the files are not actually missing we can move forward with R39 and aim to resolve this issue with R40/R41