GSE226314 - CardiacFunctionalRecovery

[idazucchi]

Project short name:

CardiacFunctionalRecovery

Primary Wrangler:

Ida

Secondary Wrangler:

arsenios

Associated files

• Google Drive: folder

Published study links

• Paper: Defining cardiac functional recovery in end-stage heart failure at single-cell resolution

• Accessioned data: GSE226314

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]

Donors

there are 3 donors in GEO that are not described in the supplementary table, so I'm including them with minimal metadata. ETOH Hx --> alcohol history y/n - the information is extremly vague and doesn't match our metadata format. I would skip this but please tell me what you think substance abuse --> description? is there a specific term for the types of Cardiomyopathy or just Cardiomyopathy?

[idazucchi]

ready for secondary review

[arschat]

Hey Ida! Well done wrangling this project too, I have some minor comments. I have uploaded the metadata of the rds file in the google drive folder just in case it is needed, since the rds is quite big to open locally.

Project - contributors

• Typo in institute of Christoph,,Kuppe and Rafael,,Kramann

Donor

• substance abuse we don't have a field for that, it could be recorded in the description

• alcolhol abuse is indeed very vague but I would record that information since the field allows such flexibility Here is a list with all biomaterials with this field filled, in which for almost half of them the value is not units/day.

  Alcohol History field

  `5cdd1fd5d96dad00085af1e6` No alcoholism reported `5cdd1fd5d96dad00085af1e7` No alcoholism reported `5cdd1fd5d96dad00085af1e8` No alcoholism reported `5cdd1fd5d96dad00085af1e9` No alcoholism reported `5cdd1fd5d96dad00085af1ea` No alcoholism reported `5cdd1fd5d96dad00085af1eb` No alcoholism reported `5cdd1fd6d96dad00085af1ec` No alcoholism reported `5cdd1fd6d96dad00085af1ed` No alcoholism reported `5cdd1fd6d96dad00085af1ee` No alcoholism reported `5cdd1fd6d96dad00085af1ef` No alcoholism reported `5cdd1fd6d96dad00085af1f0` No alcoholism reported `5cdd1fd6d96dad00085af1f1` No alcoholism reported `5cdd1fd6d96dad00085af1f2` No alcoholism reported `5d76adf5aa252400084a0d3a` Yes, amount unknown `5d76adf5aa252400084a0d3b` 4-6 per week `5d850511bddf5d0008993518` daily (alcoholic) `5d850511bddf5d0008993519` not reported `5d850511bddf5d000899351a` socially `5d850511bddf5d000899351b` heavy `5d850511bddf5d000899351c` not reported `5f0f273432d8c765c3fdfa33` unknown `5f0f273432d8c765c3fdfa34` <1U/day (for 20 years) `5f1b0ea3fe9c934c8b835c82` non-drinker `5f1b0ea3fe9c934c8b835c84` <1u/day for 30 years `5f1b0ea3fe9c934c8b835c85` <1u/day `5f1b0ea3fe9c934c8b835c86` 1-2u/day for 50 years `5f1b0ea3fe9c934c8b835c87` <1u/day `5f1b0ea3fe9c934c8b835c88` 3-6u/day for 41 years `5f1b0ea3fe9c934c8b835c89` >9U/day for 20 years `5f2bea2a4f36d156a8be1a48` <1u/day `5f2bea2a4f36d156a8be1a49` <1u/day `5f2bea2a4f36d156a8be1a4a` 3-6u/day fo 41 years `5f2bea2a4f36d156a8be1a4b` unknown units but previously a heavy drinker for 25 years `5f2bea2a4f36d156a8be1a4c` non-drinker `5f2bea2a4f36d156a8be1a4d` non-drinker `5f5fa002db657458f1bdc3b8` <1u/day `5f5fa002db657458f1bdc3c5` non-drinker `5f5fa002db657458f1bdc3c6` <1u/day `602e967491708e06ec03296b` Occassional `602e967491708e06ec03296c` Yes `602e967491708e06ec03296d` No `602e967491708e06ec03296e` Occassional `602e967491708e06ec03296f` Occassional `602e967491708e06ec032970` Yes `602e967491708e06ec032973` No `602e967491708e06ec032974` No `602e967491708e06ec032975` Occassional `602e967491708e06ec032976` Yes `602e967491708e06ec032977` Yes `602e967491708e06ec032979` Yes `602e967491708e06ec03297a` Occassional `602e967491708e06ec03297b` No `602e967491708e06ec03297c` No `602e967491708e06ec03297d` No `602e967491708e06ec03297e` No `602e967491708e06ec03297f` Yes `602e967491708e06ec032980` No `602e967491708e06ec032981` No `602e967491708e06ec032982` Yes `602e967491708e06ec032983` No `602e967491708e06ec032984` Yes `602e967491708e06ec032985` Yes `602e967491708e06ec032986` No `602e967491708e06ec032987` Yes `602e967491708e06ec032988` Occassional `602e967491708e06ec032989` Occassional `602e967491708e06ec03298b` Occasional `602e967491708e06ec03298c` Yes `602e967491708e06ec03298d` No `602e967491708e06ec03298e` No `602e967491708e06ec03298f` No `6050248d91708e06ec074ec0` unknown `6050248d91708e06ec074ec1` unknown `6050248d91708e06ec074ec2` unknown `6050248d91708e06ec074ec3` unknown `6050248e91708e06ec074ec4` unknown `6050248e91708e06ec074ec5` unknown `6050248e91708e06ec074ec6` unknown `6050248e91708e06ec074ec7` unknown `6050248e91708e06ec074ec8` unknown `6050248e91708e06ec074ec9` unknown `60c1df436c83615dd894498a` 1 unit/week `623c613fb06b223527d25e98` 1-2u/day for 50 years `623c613fb06b223527d25e99` <1u/day for 10 years `623c613fb06b223527d25e9a` 3-6u/day for 41 years `623c613fb06b223527d25e9c` nondrinker `623c613fb06b223527d25e9d` nondrinker `624d8df5b06b223527d4d5d6` 1-2 alcohol units per day `624d8df5b06b223527d4d5d9` 4 alcohol units per day `624d8df5b06b223527d4d5e7` 6 alcohol units per day `62f0ef509e42135dda854a3f` 0 alcohol units/day `62f0ef509e42135dda854a40` 0 alcohol units/day `62f0ef509e42135dda854a41` 0 alcohol units/day `62f0ef509e42135dda854a42` 0 alcohol units/day `62f0ef509e42135dda854a43` 0 alcohol units/day `62f0ef509e42135dda854a44` 0 alcohol units/day `62f0ef509e42135dda854a45` 0 alcohol units/day `62f0ef509e42135dda854a46` 0 alcohol units/day `62f0ef509e42135dda854a47` 0 alcohol units/day `633c2c3980fa451243ce2790` 1-2 units/day for 50 years `633c2c3980fa451243ce2791` <1unit/day for 10 years `633c2c3980fa451243ce2792` >9units/day for 20 years `633c2c3980fa451243ce2793` 1-2units/day for 35 years `633c2c3980fa451243ce2794` nondrinker `633c2c3980fa451243ce2795` 3-6units/day for 20 years `633c2c3980fa451243ce2796` 3-6units/day for 40 years `633c2c3980fa451243ce2797` <1unit/day for 45 years `64260264c99baf0c6c9f1d67` 0.3 drink per day `64260264c99baf0c6c9f1d68` 1 drink per day `64260264c99baf0c6c9f1d69` 1.1 drink per day `64260264c99baf0c6c9f1d6e` 1.4 drink per day `64260264c99baf0c6c9f1d75` 0.6 drink per day `64260265c99baf0c6c9f1d76` 1 drink per day `64260265c99baf0c6c9f1d7a` 2 drink per day `64260265c99baf0c6c9f1d7c` 2 drink per day `64260265c99baf0c6c9f1d7d` 1.7 drink per day `64260265c99baf0c6c9f1d7e` 0.3 drink per day `64260265c99baf0c6c9f1d7f` 1.1 drink per day `64260265c99baf0c6c9f1d81` 0.7 drink per day `64260265c99baf0c6c9f1d82` 0.6 drink per day `64260265c99baf0c6c9f1d86` 2 drink per day `64260266c99baf0c6c9f1d8c` 1.4 drink per day `64260266c99baf0c6c9f1d8d` 1.4 drink per day `64260266c99baf0c6c9f1d92` 2 drink per day `64260266c99baf0c6c9f1d96` 0.4 drink per day `64260266c99baf0c6c9f1d97` 0.1 drink per day `64260266c99baf0c6c9f1d99` 0.4 drink per day `64260266c99baf0c6c9f1d9c` 2 drink per day `64260267c99baf0c6c9f1d9d` 0.1 drink per day `64260267c99baf0c6c9f1d9e` 0.4 drink per day `64260267c99baf0c6c9f1da1` 2 drink per day `64260267c99baf0c6c9f1da2` 2 drink per day `64260267c99baf0c6c9f1da4` 0.4 drink per day `64260267c99baf0c6c9f1da7` 2.1 drink per day `64260267c99baf0c6c9f1da9` 0.1 drink per day `64260268c99baf0c6c9f1db3` 0.3 drink per day `64260268c99baf0c6c9f1db7` 3 drink per day `64260268c99baf0c6c9f1db8` 1 drink per day `64260268c99baf0c6c9f1dba` 1.4 drink per day `64260268c99baf0c6c9f1dbf` 0.6 drink per day `64260269c99baf0c6c9f1dc5` 0.9 drink per day `64260269c99baf0c6c9f1dc7` 0.7 drink per day `64260269c99baf0c6c9f1dc8` 0.7 drink per day `6446bfe35178b3171274db7b` <1 unit/day `6446bfe35178b3171274db7c` <1 unit/day `6446bfe35178b3171274db7d` >9 units/day `6446bfe35178b3171274db7e` >9 units/day `6446bfe35178b3171274db7f` 2 units/day `6446bfe35178b3171274db80` <1 unit/day `6446bfe35178b3171274db81` <1 unit/day `6446bfe35178b3171274db84` >3 units/day `6446bfe35178b3171274db85` <1 unit/day `6446bfe35178b3171274db86` <1 unit/day `65201cd7fb47305198b91797` history of alcohol abuse `656a01847741856bcf3c7e18` 3-6 units/day, 40 years `656a01847741856bcf3c7e19` 1 unit/day `656a01857741856bcf3c7e1a` Heavy drinker 25 years but units/day unknown `656a01867741856bcf3c7e1b` 3-6 units / day, 20 years `656a01877741856bcf3c7e1c` 0 `656a01877741856bcf3c7e1d` 1 unit/day, 30 years `656a01887741856bcf3c7e1e` 1-2 units/day, 20 years `656a01897741856bcf3c7e1f` 0 `656a01897741856bcf3c7e20` 1 unit/day, 30 years `656a018a7741856bcf3c7e21` 1 unit / day, 50 years `656a018b7741856bcf3c7e22` 7-9units/day `656a018b7741856bcf3c7e23` 7-9 units/day `656a018c7741856bcf3c7e24` 1-2 units/day, 50 years `656a018d7741856bcf3c7e25` 1 unit/day

Library preparation

• the cell barcode length is 14. However, in this document, the "Single Cell 5' Gene Expression Libraries (v1 and v1.1)" specifies that Read 1 which contain cell barcode + UMI has 26 bp length. I am not 100% sure about this, and the teichman lab page does not specify structure for 5' GEX v1.1. Let me know what you think.

Analysis files

• you could specify the matrix cell count for the analysis file:

  62459 features across 185881 samples within 2 assays RNA (33694 features, 0 variable features SCT (28765 features, 3000 variable features)

• you could specify the file source of the data (GEO)

[idazucchi]

thanks for the review! I've applied the suggestions and started the export

[idazucchi]

|| were found during the indexing process, I've updated the project and re-released for R37

[idazucchi]

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