Arc Virtual Cell Atlas: scRNA-seq¶
The Arc Virtual Cell Atlas hosts one of the biggest collections of scRNA-seq datasets.
Lamin mirrors the dataset for simplified access here: https://lamin.ai/laminlabs/arc-virtual-cell-atlas
If you use the data academically, please cite the original publications, Youngblut et al. (2025) and Zhang et al. (2025).
Connect to the instance:
# pip install 'lamindb[jupyter,bionty,wetlab,gcp]'
!lamin connect laminlabs/arc-virtual-cell-atlas
Show code cell output
→ connected lamindb: laminlabs/arc-virtual-cell-atlas
import lamindb as ln
import bionty as bt
import wetlab as wl
Show code cell output
→ connected lamindb: laminlabs/arc-virtual-cell-atlas
Metadata¶
21 organisms.
bt.Organism.df()
| uid | name | ontology_id | scientific_name | synonyms | description | space_id | source_id | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | 7PRZ0StI | thale-cress | NCBITaxon:3702 | Arabidopsis thaliana | thale cress|mouse-ear cress | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 2 | NY4Fwo6n | dairy cow | NCBITaxon:9913 | Bos taurus | ox|oxen|bovine|domestic cow|cattle|cow|domesti... | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 3 | 5CDgMx83 | caenorhabditis elegans | NCBITaxon:6239 | Caenorhabditis elegans | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 4 | 3qUn9Zrd | white-tufted-ear marmoset | NCBITaxon:9483 | Callithrix jacchus | white ear-tufted marmoset|common marmoset | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 5 | 7bjJiyyC | zebra danio | NCBITaxon:7955 | Danio rerio | zebra fish|leopard danio|zebrafish | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 6 | 5JGkUUo0 | fruit fly | NCBITaxon:7227 | Drosophila melanogaster | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 7 | s7OX44As | equine | NCBITaxon:9796 | Equus caballus | horse|domestic horse | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 8 | 4fzSxbbW | chicken | NCBITaxon:9031 | Gallus gallus | Gallus domesticus|chickens|bantam | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 9 | 38ZOM8IO | western gorilla | NCBITaxon:9593 | Gorilla gorilla | gorilla | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 10 | 2R9u9P71 | naked mole rat | NCBITaxon:10181 | Heterocephalus glaber | naked mole-rat | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 11 | 1dpCL6Td | human | NCBITaxon:9606 | Homo sapiens | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 12 | 2AmW7N1E | rhesus macaque | NCBITaxon:9544 | Macaca mulatta | rhesus monkeys|rhesus macaques|Rhesus monkey | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 13 | 3RZqbcSL | house mouse | NCBITaxon:10090 | Mus musculus | mouse | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 14 | 2cmrlaa8 | european rabbit | NCBITaxon:9986 | Oryctolagus cuniculus | rabbits|rabbit|Japanese white rabbit|domestic ... | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 15 | 6mtjopSB | asian cultivated rice | NCBITaxon:4530 | Oryza sativa | rice|red rice | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 16 | 1e0pqlXq | wild sheep | NCBITaxon:9940 | Ovis aries | sheep|lambs|domestic sheep | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 17 | 4V2ejovf | chimpanzee | NCBITaxon:9598 | Pan troglodytes | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 18 | 5lgRwIC9 | schistosoma mansoni | NCBITaxon:6183 | Schistosoma mansoni | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 19 | 2Dgc0iBG | tomato | NCBITaxon:4081 | Solanum lycopersicum | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 20 | 7N29aZih | swine | NCBITaxon:9823 | Sus scrofa | wild boar|pigs|pig | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
| 21 | 70VIwHUJ | maize | NCBITaxon:4577 | Zea mays | None | None | 1 | 10 | 2 | 2025-02-25 20:05:50.334478+00:00 | 1 | None | 1 |
50 cell lines.
bt.CellLine.df()
Show code cell output
| uid | name | ontology_id | abbr | synonyms | description | space_id | source_id | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | 505Oto0b | NCI-H1573 | CVCL_1478 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 2 | 2yrJ1RO9 | NCI-H460 | CVCL_0459 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 3 | 729jQiCV | hTERT-HPNE | CVCL_C466 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 4 | 2MwkQgWO | SW48 | CVCL_1724 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 5 | 6SFnBlyJ | HOP62 | CVCL_1285 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 6 | 39vFskbz | NCI-H1792 | CVCL_1495 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 7 | 3Yy5mGIS | SW480 | CVCL_0546 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 8 | 1p59Uds7 | HT-29 | CVCL_0320 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 9 | 7KUHx7VC | LoVo | CVCL_0399 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 10 | 4Ch2fV9a | Hs 766T | CVCL_0334 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 11 | 65gF96lU | PANC-1 | CVCL_0480 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 12 | 6h8KcJYp | MIA PaCa-2 | CVCL_0428 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 13 | 7aEsdKjg | SW 1271 | CVCL_1716 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 14 | 4n6gUGHY | RKO | CVCL_0504 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 15 | 1v7Mehiu | H4 | CVCL_1239 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 16 | HLBTHKPg | SW1417 | CVCL_1717 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 17 | tdp1HNAN | CFPAC-1 | CVCL_1119 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 18 | 5Jp9rqX7 | SW 900 | CVCL_1731 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 19 | 5Vjc1Ubr | KATO III | CVCL_0371 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 20 | EtRJf7f9 | C-33 A | CVCL_1094 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 21 | 18kaNqu0 | SNU-1 | CVCL_0099 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 22 | 4IfJB0Y2 | J82 | CVCL_0359 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 23 | 3PDtUj4s | A-172 | CVCL_0131 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 24 | NvPXo2Hu | SHP-77 | CVCL_1693 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 25 | 5N1doHnP | SNU-423 | CVCL_0366 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 26 | 6GOSOOui | HS-578T | CVCL_0332 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 27 | 7QShig8F | A498 | CVCL_1056 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 28 | 6NWX3dtq | NCI-H2347 | CVCL_1550 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 29 | VEd9akJo | LOX-IMVI | CVCL_1381 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 30 | bC8JbRlg | NCI-H23 | CVCL_1547 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 31 | 5ewuYry0 | Panc 03.27 | CVCL_1635 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 32 | 1CdEQ5dJ | LS 180 | CVCL_0397 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 33 | 1mLuzzow | HEC-1-A | CVCL_0293 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 34 | 63ZWvcHV | HCT15 | CVCL_0292 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 35 | 5XupQdHO | COLO 205 | CVCL_0218 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 36 | 4hyU9oFu | BT-474 | CVCL_0179 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 37 | 5lqReFKR | AN3 CA | CVCL_0028 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 38 | 1lhqeW2v | RPMI-7951 | CVCL_1666 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 39 | 39rNVaPP | SK-MEL-2 | CVCL_0069 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 40 | vEfTp1Hk | A549 | CVCL_0023 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 41 | 4QH2SpWA | NCI-H2030 | CVCL_1517 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 42 | 1K1CzNSi | C32 | CVCL_1097 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 43 | 3Oz9gRsu | HepG2/C3A | CVCL_1098 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 44 | 5JZNtoDJ | AsPC-1 | CVCL_0152 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 45 | 2eQosYls | CHP-212 | CVCL_1125 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 46 | 219BOZMe | SW 1088 | CVCL_1715 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 47 | 6O2MPQMm | A-427 | CVCL_1055 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 48 | J5Ylm8TV | NCI-H2122 | CVCL_1531 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 49 | 7dL2LJjx | NCI-H661 | CVCL_1577 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
| 50 | 7VaGVBNB | NCI-H596 | CVCL_1571 | None | None | None | 1 | None | 3 | 2025-02-25 22:20:20.217993+00:00 | 1 | None | 1 |
100 compounds.
wl.Compound.df()
Show code cell output
| uid | name | ontology_id | chembl_id | abbr | synonyms | description | space_id | source_id | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 380 | JRDV3CsZ | Tolmetin | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 379 | x3BfjX6J | Peretinoin | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 378 | 18PJ8Lu8 | Niclosamide (olamine) | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 377 | 5yeFtKHy | Apalutamide | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 376 | 2AEfoFfq | Mifepristone | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 285 | enh3vp0f | Ixazomib | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 284 | 4iDSuajq | Pimitespib | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 283 | 5y8FwPtA | 4EGI-1 | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 282 | 5lagGAeu | Torkinib | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
| 281 | 1NkoYXbq | Tubulin inhibitor 6 | None | None | None | None | None | 1 | None | 3 | 2025-02-25 22:48:58.568677+00:00 | 1 | None | 1 |
100 rows × 14 columns
The Tahoe collection¶
Every individual dataset in the atlas is an .h5ad file that is registered as an artifact in LaminDB.
Let us first query for the Tahoe collection.
collection = ln.Collection.get(key="tahoe100")
collection.artifacts.df()
Show code cell output
! no run & transform got linked, call `ln.track()` & re-run
! run input wasn't tracked, call `ln.track()` and re-run
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1369 | XVSrkq9pyF1OBLgG0000 | 2025-02-25/h5ad/plate3_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 13173722269 | Jnrt7DaSUCGn8D8LS2itaw | None | 4705402 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.497965+00:00 | 1 | None | 1 |
| 1366 | vn5cUJCHbjpPPsZx0000 | 2025-02-25/h5ad/plate14_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 22427932564 | FrnStRehP16siRGG35ou+g | None | 6518806 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:19.357999+00:00 | 1 | None | 1 |
| 1362 | 56uA9lPPmJ4zLUcr0000 | 2025-02-25/h5ad/plate10_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 26536400717 | j1FXsX7hs7u+eBqnWnmNHw | None | 8044908 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:17.849980+00:00 | 1 | None | 1 |
| 1365 | 9L9HZ55HqUL0aqaR0000 | 2025-02-25/h5ad/plate13_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 28071589885 | RKOiaay+CHvv+Ukk/N+28A | None | 8501658 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.977981+00:00 | 1 | None | 1 |
| 1372 | aAHQ3zbD7n1asyYr0000 | 2025-02-25/h5ad/plate6_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 28934897078 | NYvQEqVClziHm0ozWhOw1w | None | 7545393 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:21.629962+00:00 | 1 | None | 1 |
| 1373 | DC5cacdJr1VoEXnl0000 | 2025-02-25/h5ad/plate7_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 16514746341 | NOS4MY6eYYPOnAB8ViyWYg | None | 5692117 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.009157+00:00 | 1 | None | 1 |
| 1375 | BDttiuV3Te8VB0dU0000 | 2025-02-25/h5ad/plate9_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 18791302576 | 4kHbVbmreg6akW6ZgsjxaA | None | 5866669 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.759201+00:00 | 1 | None | 1 |
| 1374 | czC19UpUEszVH2bU0000 | 2025-02-25/h5ad/plate8_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 30390935958 | ilAzEPIh4FlDeTFaJ1dILw | None | 8880979 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.387666+00:00 | 1 | None | 1 |
| 1370 | tKTeff0ugWqAm4P70000 | 2025-02-25/h5ad/plate4_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 23292672278 | BkBXznbSovNWXtzPFITPcQ | None | 7004356 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.879928+00:00 | 1 | None | 1 |
| 1371 | EZATJLC4jE7pmwo40000 | 2025-02-25/h5ad/plate5_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 19763140865 | VMBKFzOI5cj7UC1UDENP4A | None | 6419498 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:21.255154+00:00 | 1 | None | 1 |
| 1367 | aJIqo7bNyJAs9z0r0000 | 2025-02-25/h5ad/plate1_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 19070623904 | 9iCNcouMqfNS3HA/2GUWOA | None | 5481420 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:19.737995+00:00 | 1 | None | 1 |
| 1364 | S2h2rPLCaUhZAM9u0000 | 2025-02-25/h5ad/plate12_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 37495736876 | VjAkWVFGVpzAMi9Innusuw | None | 10487057 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.600910+00:00 | 1 | None | 1 |
| 1368 | ZFeVfd0ugAHeWCxm0000 | 2025-02-25/h5ad/plate2_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 29037152127 | usxviuqGbuw0RYnECCVCWw | None | 8064658 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.113956+00:00 | 1 | None | 1 |
| 1363 | omn7JStfJMzy8m6O0000 | 2025-02-25/h5ad/plate11_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 23230802756 | N2mzoYlMLEl6PdecaYyDvw | None | 7435869 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.229629+00:00 | 1 | None | 1 |
Each of the datasets were validated with the same schema:
schema = ln.Schema.get(name="tahoe100_anndata_schema")
ln.Artifact.filter(schema=schema).df()
Show code cell output
| uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||||||
| 1369 | XVSrkq9pyF1OBLgG0000 | 2025-02-25/h5ad/plate3_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 13173722269 | Jnrt7DaSUCGn8D8LS2itaw | None | 4705402.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.497965+00:00 | 1 | None | 1 |
| 1366 | vn5cUJCHbjpPPsZx0000 | 2025-02-25/h5ad/plate14_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 22427932564 | FrnStRehP16siRGG35ou+g | None | 6518806.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:19.357999+00:00 | 1 | None | 1 |
| 1362 | 56uA9lPPmJ4zLUcr0000 | 2025-02-25/h5ad/plate10_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 26536400717 | j1FXsX7hs7u+eBqnWnmNHw | None | 8044908.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:17.849980+00:00 | 1 | None | 1 |
| 1365 | 9L9HZ55HqUL0aqaR0000 | 2025-02-25/h5ad/plate13_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 28071589885 | RKOiaay+CHvv+Ukk/N+28A | None | 8501658.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.977981+00:00 | 1 | None | 1 |
| 1372 | aAHQ3zbD7n1asyYr0000 | 2025-02-25/h5ad/plate6_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 28934897078 | NYvQEqVClziHm0ozWhOw1w | None | 7545393.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:21.629962+00:00 | 1 | None | 1 |
| 1373 | DC5cacdJr1VoEXnl0000 | 2025-02-25/h5ad/plate7_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 16514746341 | NOS4MY6eYYPOnAB8ViyWYg | None | 5692117.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.009157+00:00 | 1 | None | 1 |
| 1375 | BDttiuV3Te8VB0dU0000 | 2025-02-25/h5ad/plate9_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 18791302576 | 4kHbVbmreg6akW6ZgsjxaA | None | 5866669.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.759201+00:00 | 1 | None | 1 |
| 15 | 3Yl20zyG926CkvP50000 | 2025-02-25/tutorial/plate3_2k-obs.h5ad.gz | None | .h5ad.gz | dataset | AnnData | 7253540 | vv16qryJsVY98jDBqhkr9w | None | NaN | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 19:31:01.255128+00:00 | 1 | None | 1 |
| 1374 | czC19UpUEszVH2bU0000 | 2025-02-25/h5ad/plate8_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 30390935958 | ilAzEPIh4FlDeTFaJ1dILw | None | 8880979.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:22.387666+00:00 | 1 | None | 1 |
| 1370 | tKTeff0ugWqAm4P70000 | 2025-02-25/h5ad/plate4_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 23292672278 | BkBXznbSovNWXtzPFITPcQ | None | 7004356.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.879928+00:00 | 1 | None | 1 |
| 1371 | EZATJLC4jE7pmwo40000 | 2025-02-25/h5ad/plate5_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 19763140865 | VMBKFzOI5cj7UC1UDENP4A | None | 6419498.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:21.255154+00:00 | 1 | None | 1 |
| 1367 | aJIqo7bNyJAs9z0r0000 | 2025-02-25/h5ad/plate1_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 19070623904 | 9iCNcouMqfNS3HA/2GUWOA | None | 5481420.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:19.737995+00:00 | 1 | None | 1 |
| 1364 | S2h2rPLCaUhZAM9u0000 | 2025-02-25/h5ad/plate12_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 37495736876 | VjAkWVFGVpzAMi9Innusuw | None | 10487057.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.600910+00:00 | 1 | None | 1 |
| 1368 | ZFeVfd0ugAHeWCxm0000 | 2025-02-25/h5ad/plate2_filt_Vevo_Tahoe100M_WSe... | None | .h5ad.gz | dataset | AnnData | 29037152127 | usxviuqGbuw0RYnECCVCWw | None | 8064658.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:20.113956+00:00 | 1 | None | 1 |
| 1363 | omn7JStfJMzy8m6O0000 | 2025-02-25/h5ad/plate11_filt_Vevo_Tahoe100M_WS... | None | .h5ad.gz | dataset | AnnData | 23230802756 | N2mzoYlMLEl6PdecaYyDvw | None | 7435869.0 | md5 | False | False | 1 | 2 | 3 | None | True | 1 | 2025-02-25 23:22:18.229629+00:00 | 1 | None | 1 |
Here is how the features in the dataset look like:
artifact = ln.Artifact.filter(schema=schema).first() # the first in the collection
artifact.describe()
Artifact .h5ad.gz/AnnData ├── General │ ├── .uid = 'XVSrkq9pyF1OBLgG0000' │ ├── .key = '2025-02-25/h5ad/plate3_filt_Vevo_Tahoe100M_WServicesFrom_ParseGigalab.h5ad.gz' │ ├── .size = 13173722269 │ ├── .hash = 'Jnrt7DaSUCGn8D8LS2itaw' │ ├── .n_observations = 4705402 │ ├── .path = gs://arc-ctc-tahoe100/2025-02-25/h5ad/plate3_filt_Vevo_Tahoe100M_WServicesFrom_ParseGigalab.h5ad.gz │ ├── .created_by = sunnyosun (Sunny Sun) │ ├── .created_at = 2025-02-25 23:22:20 │ └── .transform = 'Register Tahoe-100M' ├── Dataset features/schema │ ├── var • 62710 [bionty.Gene.stable_id] │ │ TSPAN6 int │ │ TNMD int │ │ DPM1 int │ │ SCYL3 int │ │ C1orf112 int │ │ FGR int │ │ CFH int │ │ FUCA2 int │ │ GCLC int │ │ NFYA int │ │ STPG1 int │ │ NIPAL3 int │ │ LAS1L int │ │ ENPP4 int │ │ SEMA3F int │ │ CFTR int │ │ ANKIB1 int │ │ CYP51A1 int │ │ KRIT1 int │ │ RAD52 int │ └── obs • 16 [Feature] │ cell_line cat[bionty.CellLine.onto… A-172, A-427, A498, A549, AN3 CA, AsPC-1… │ cell_name cat[bionty.CellLine] A-172, A-427, A498, A549, AN3 CA, AsPC-1… │ drug cat[wetlab.Compound] 4EGI-1, 9-ING-41, APTO-253, AT7519, AZD-… │ drugname_drugconc cat[wetlab.CompoundPertu… [('4EGI-1', 5.0, 'uM')], [('9-ING-41', 5… │ pass_filter cat[ULabel[PassFilter]] full, minimal │ phase cat[ULabel[Phase]] G1, G2M, S │ plate cat[ULabel[Plate]] plate3 │ sample cat[wetlab.Biosample] smp_1687, smp_1688, smp_1689, smp_1690, … │ gene_count int │ tscp_count int │ mread_count int │ pcnt_mito float │ S_score float │ G2M_score float │ sublibrary str │ BARCODE str └── Labels └── .references Reference Tahoe-100M: A Giga-Scale Single-Cell Per… .compounds wetlab.Compound NG25, venetoclax, Gemcitabine, PH-797804… .compound_perturbations wetlab.CompoundPerturbat… [('Pemigatinib', 5.0, 'uM')], [('Belzuti… .biosamples wetlab.Biosample smp_1760, smp_1764, smp_1754, smp_1743, … .organisms bionty.Organism human .cell_lines bionty.CellLine Panc 03.27, PANC-1, NCI-H460, HEC-1-A, M… .ulabels ULabel tahoe-100, plate3, G1, G2M, S, full, min…
The genes are indexed with a “stable ID”, a unique mix of Ensembl gene ID and gene symbol.
Every AnnData object measures a broad range of perturbations, biosamples and cell lines. The plates are approximate replicates for each other.
You can download an .h5ad into your local cache like so:
artifact.cache()
Note that unlike what the suffix suggests, the .h5ad is presently not compressed.