SCP1479 - CrossTissueNucleiEraslan

[arschat]

Project short name:

CrossTissueNucleiEraslan Segr-Human-10x3pv2

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

• Google Drive: folder
• Ingest: c14f788a-a438-459d-b470-ccb65e9e259e

Published study links

• Paper: 10.1126/science.abl4290

• Accessioned data: SCP1479 phs000424 anvil.terra.bio/ (managed access)

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

[arschat]

Notes

• Although no cause of death is defined for any of the donors, all donors have 0 (ventilator case) in hardy scale. This information is derived from the public metadata of the GTEx portal of the corresponding fixed tissue from the same donor that is provided in the supplementary table 1 (example wait for some seconds) This information is also contained in the GTEx portal in the file GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt

• I tried to use useful IDs for all 3 biomaterials:

  • donor_id: the unique identifier of the donors of GTEx project GTEX-12BJ1
  • specimen_from_organism_ID: a combination of tissue and the individual ID within tissue breast_01
  • cell_suspension: the tissue-individual-prep of the adata.obs which is the specimen_from_organism but with different dissociation protocol used skeletalmuscle_01_CST besides that, alternative names have been filled in the biomaterial_name of each biomaterial

• Sequencing machine is not clear. Manuscript methods:

  Libraries for snRNA-seq were generated using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics), and sequencing was performed with Illumina HiSeq X (96 samples) or NextSeq (three samples), according to the manufacturer’s protocols.

  However, there are three problems:

  • there are only 95 samples adata.obs['channel'] in the files
  • there is no mention on which 3 samples were sequenced in NextSeq
  • the model of NextSeq is not specified (for example NextSeq 500 or 2000)

  Supplementary materials (page 5):

  Libraries were sequenced on an Illumina HiSeq X or NextSeq

  Sending contributors email to clarify We should not get in contact with the authors of wave 2 yet.

[arschat]

Sequencing machine not clear. Manuscript methods:

Libraries for snRNA-seq were generated using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics), and sequencing was performed with Illumina HiSeq X (96 samples) or NextSeq (three samples), according to the manufacturer’s protocols.

However, there are three problems:

• there are only 95 samples adata.obs['channel'] in the files
• there is no mention on which 3 samples were sequenced in NextSeq
• the model of NextSeq is not specified (for example NextSeq 500 or 2000)

Supplementary materials (page 5):

Libraries were sequenced on an Illumina HiSeq X or NextSeq

Sending contributors email to clarify We should not get in contact with the authors of wave 2 yet.

[arschat]

Besides the sequencer inconsistency mentioned before, I have filed the dataset for verification using only the first of the two sequencers mentioned. Before final submission, I will discuss that internally.

Graph valid and ready for sec review.

[idazucchi]

Hi Arsenios! Nice job on this dataset! I only have a few comments

Specimen

• are the ids you're using matching those in the h5ad? if not I would reuse the publiaction's
• for esophagus samples: I would use esophagus mucosa UBERON:0002469 and smooth muscle of esophagus UBERON:0002112

Dissociation

• dissociation seems more mechanical (pestle/scissors) or enzyme-free chemical dissociation since they're using detergent to break down the membrane

Cell suspension

• description is missing
• Are the pooled samples missing from the h5ad?

Library prep

• primer should be poly-dT

[arschat]

Applied changes.

• Changed the biomaterial_ID in both specimen & cell suspension to match Sample ID and channel columns respectively. Alternative name is in biomaterial_name
• Added also mechanical dissociation protocols and changed existing to enzyme-free chemical dissociation
• Pooled samples are not present (or presented as distinct samples) in h5ad. No pooling is mentioned in any of the adata.obs columns

Submission is now in graph valid. As discussed in standup we will wait for the first contact to authors to verify the sequence machine of all samples.

[arschat]

the pre-print of this publication has been already published in DCP ingest link