schirmerSpatialMS

[arschat]

Handed over from UCSC team (mail thread)

Project short name:

schirmerSpatialMS

Primary Wrangler:

Arsenios

Secondary Wrangler:

Ida

Associated files:

spreadsheet

• Google Drive: folder, latest spreadsheet
• ingest: 4c8e9d75-d85a-47de-9598-06549cf44b91

Key Events

• [ ] Send initial instructions about contributing, including questionnaire and T&Cs
• [ ] Receive project questionnaire
• [ ] Assign the Primary Wrangler
• [ ] Receive T&C form filled out by at least 1 representative of group/project
• [ ] Send custom metadata template spreadsheet, how-to guide and directions for submitting data, matrix and cell annotation files.
• [ ] Receive spreadsheet (to a sufficient standard to submit dataset)
• [ ] Receive data, matrix and cell annotation files (to a sufficient standard to submit dataset)
• [ ] Curate metadata spreadsheet with ontologies
• [ ] Upload sheet to validate metadata
• [ ] Run graph validator & Check linking
• [ ] Validate data files
• [ ] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [ ] Get final approval of submission from the contributor including release date, metadata spreadsheet and data files
• [ ] Submit to production and inform ingest-devs the project is ready for archiving
• [ ] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

Please track the below as well as the key events:

1. Track date first spreadsheet received and final spreadsheet sent by editing ticket to include date next to event.
2. Track spreadsheet iterations by placing asterisks next to receive spreadsheet event.
3. Track any metadata issues/tickets made for dataset with a bulleted list of links under received spreadsheet event. Links should be to the ticket in the metadata repo.

[arschat]

Will verified that they've sent the credentials.

hca-util upload area 7373e619-39dc-45ca-8357-d739a6cc5445

• [x] contributor uploads files
• [x] validate files
• [x] review spreadsheet
• [x] graph valid
• [x] sec reviewed
• [ ] exported
• [ ] import form sent

[arschat]

Contributor was not sure of the modelling for the experimental design. I will share the following with them, hopeful that they wont get more confused.

flowchart TD
    A(["Donor organism"]) -- Collection protocol --> B(["Specimen from Organism"])
    B -- Image preparation protocol --> C(["Imaged specimen"])
    B -- Dissociation protocol --> D(["Cell suspension"])
    C -- Imaging protocol --> G("Image file")
    C -- Sequencing protocol --> E("Sequence file")
    D -- Sequencing protocol --> E
    C -- Analysis protocol --> F("Analysis file")
    D -- Analysis protocol --> F

[arschat]

Verified the modality of each sample:	snRNA	visium
CO37	x	x
CO40	x	x
CO41	x	x
CO45	x
CO74	x	x
CO85	x	x
CO96		x
MS94		x
MS197D	x	x
MS197U		x
MS229	x	x
MS377N	x	x
MS377T	x	x
MS377I	x	x
MS411	x	x
MS497I	x	x
MS497T	x	x
MS549H	x	x
MS549T	x	x

[idazucchi]

Hello! I'm done with the review It looks great, I have only minor comments

project

Is the project marked as NRES? It's not in the spreadsheet

imaging protocol

minor detail, but the description includes all the analysis too, is this intentional?

image file

imaged_speciment_MS377N doesn't have the 2 png jpeg json block

dissociation protocol

The description mentions muscle dissociation rather than brain tissue and includes imaging prep description, is this the correct protocol?

library prep

10x v3 is missing the cell barcode fields

analysis file

there is some difference in the type of files offered for different imaged specimens most of them have a set of 5, except for imaged_speciment_MS377N who only has 3 and then these have one set of 3 plus a set of 5

• imaged_speciment_CO96
• imaged_speciment_MS94
• imaged_speciment_MS197U

do you know if that's intentional?

[arschat]

Thanks a lot Ida! I've updated the spreadsheet with the ingest generated one to include all the changes done in ingest.

About the speciments with the extra analysis files,

long story

They originally uploaded all files without the prefix, and subsequently uploaded the files with the prefix to distinguish. Those 3 specimens however, do not have a transcriptomics modality. This can be verified since their ST counterparts have the same size. Therefore, I removed these 3 barcode/feature/matrix that did NOT have the ST prefix (and their processes).

short, this is not be intentional.

I replaced the typo in the specimen as well, added the cell barcode & spatial barcode, and also ontology fields for sequencer.

I am waiting for the contributor to verify that they are ok without the MS377N image files, and that the dissociation description is the correct one, and I am submitting.

[arschat]

exported and import form sent