Muzz Haniffa - Fetal Skin

[lauraclarke]

Primary Wrangler: Ami

Project ShortName: DevelopmentalCellProgramsSkin

Google Sheet: https://docs.google.com/spreadsheets/d/13kLndCrN4y2xLTGjVR6pKhEYu0SGTmwr/edit#gid=1323794650

Array Express: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8142/?query=Developmental+cell+programs+are+co-opted+in+inflammatory+skin+disease

Ingest production: https://contribute.data.humancellatlas.org/submissions/detail?id=60ed7ecfd5d575160aafa4c1 upload bucket

Key Events

• [x] translate arrayexpress metadata to hca metadata and send for review
• [x] Curate metadata spreadsheet with ontologies
• [x] Upload sheet to validate metadata (most likely in staging)
• [x] Check linking
• [ ] 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 and hand off tracking to data dashboard

[lauraclarke]

Copy of https://github.com/HumanCellAtlas/hca-data-wrangling/issues/315

[mshadbolt]

This is now an HCA publication and has a preprint here: https://www.biorxiv.org/content/10.1101/2020.11.05.369363v1

[lauraclarke]

This paper has been published https://science.sciencemag.org/content/371/6527/eaba6500 are the raw data still not available?

[mshadbolt]

It has living european donors

[ami-day]

Contacted the authors about the 10X technology version.

[ami-day]

This is stalled until either the authors get back with the technology version or we are able to add 10X as a library preparation method without specifying the barcode length and offset. There is a ticket for a metadata schema update to enable this.

[clairerye]

Not urgent, but @Wkt8 has a good relationship with Muzz so it may be worth him following up directly with her.

[Wkt8]

Assigning self as secondary reviewer.

[Wkt8]

Hey Ami! Looks good so far - just had a few optional additions and somethings I was confused about.

Donor_Organisms I think you could add (optionally) that all patients BMI range was 23-28 in donor organisms (it says so in the supplementary methods)

Collection_Protocol Patients with atopic dermatitis and psoriasis, who donated skin for single cell RNA-sequencing (scRNA-seq), consented to a 6 mm punch biopsy from lesional and non-lesional skin from the lower back (at least 2 cm away from lesional skin)

I think this is the actual collection info and the 'cutting skin to thin strips' is more of a mechanical dissociation protocol? Feel free to disagree though!

Enrichment_Protocol FACS Enrichment Protocol Description isn’t correct - I think you might have copy+pasted the mass cytometry protocol description instead. The FACS protocol is as follows:

Suspensions of dermal or epidermal cells were resuspended in 100 μl of flow buffer per 107 cells, transferred to polypropylene FACS tubes (BD Falcon, 352063) and stained with 5 μl of each antibody per 107 cells for 30 minutes at 4oC in the dark. Cells were washed by diluting in flow buffer and centrifuging at 500 x g for 5 minutes, then resuspended in 1 ml of sort buffer per 20×106 cells with 3 μM DAPI. Cells were then filtered using a 100 μm cell strainer and sorted using a FACSFusion Sorter with a 100 μm fluidics nozzle. Cells isolated from contiguously placed FACS gates shown in Fig. S1B (healthy skin) and Fig. S1C (AD and psoriasis skin) were profiled by scRNA-seq.

Library_Prep_Protocol Sorry - I’m a bit confused, I think in the paper it mentions 10x 3’, 5’ + TCR enrichment, and also Smart-Seq2 protocols. I checked the ArrayExpress accession and only the 10x 3’ information was there - does this mean the processed data for the other papers is unavailable?

Sequencing_Protocol Also ‘Yes’ to Paired end according to the sequencing_protocol.

[ami-day]

Thanks @Wkt8 I made the changes.

In terms of the collection protocol, you're right and I realise there are actually 2 different protocols: 1 for healthy, 1 for psoriasis or atopic dermatitis.

I kept the sequencing protocol "paired end" field as "no" as this is a 10X 3' dataset.

In terms of the vdj experiments and smart-seq2 experiments: they do not mention anywhere where this data is available in raw or processed form. I have messaged the scea team about it. However, they initially said that they had agreed with the authors to submit the adult data first, and create a new submission for fetal data. It might also be the case for the other technologies.

For now, I will upload this dataset for July 26th milestone, and later on, we can either update the project in ingest, or, create an additional project for the data from fetal samples and/or other technologies.

Thanks!

[ami-day]

submitted metadata and data: https://contribute.data.humancellatlas.org/submissions/detail?id=60ed7ecfd5d575160aafa4c1

[Wkt8]

Checked and confirmed that this has exported. Ami to complete the export form when she returns!

[ami-day]

Done.

[idazucchi]

Fastqs are now available in ArrayExpress - should we add them to the project?

[idazucchi]

It should be techincally possible to add the fastq files with an update but this task is low priority for two reasons:

1. the skin network is not particualrly interested in fastq files
2. we are giving priority to the first 6 draft atlases - our help is most needed for gut, brain and eyes

[ami-day]

Requires checking if fastq files can be made available for living donors

[ofanobilbao]

Re-opening this for investigation as per the discussion in Ops review meeting last week

[Wkt8]

Echoing Ida's comments above:

It should be technically possible to add the fastq files with an update (https://www.ebi.ac.uk/ena/browser/view/PRJEB33522) but this task is VERY low priority for THREE reasons:

• The skin network is not particularly interested in fastq files
• We are giving priority to the first 6 draft atlases - our help is most needed for gut, brain and eyes
• The fastq files come from living donors even though they are now available in open archives

[ofanobilbao]

We can use this Release 30, where we are focusing on Updates or datasets we down-prioritised in the past. Moving it to Needs Update to pick up for this release

[Wkt8]

Value added is very small for the amount of work required, as the metadata is already linked to the fastqs in ArrayExpress.