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merged 5 commits into from
Dec 23, 2024
Merged

feat: publish neural organoid atlas on the atlas page (#2622) #2624

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69a92dc
feat: publish neural organoid atlas on the atlas page (#2622)
Dec 12, 2024
57e3154
feat: update neural organoid publication (#2622)
Dec 13, 2024
6f6b968
feat: updated organoid description (#2622)
Dec 17, 2024
3bbe095
feat: updated source dataset estimated cell with default value '--' (…
Dec 17, 2024
a092bfb
feat: updated organoid neural description and newly published source …
Dec 18, 2024
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1 change: 1 addition & 0 deletions @types/network.ts
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Expand Up @@ -183,6 +183,7 @@ export type AtlasKey =
| "brain-v1-0"
| "cortex-v1-0"
| "lung-v1-0"
| "organoid-neural-v1-0"
| "retina-v1-0";

export interface BICCNPublication {
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2 changes: 1 addition & 1 deletion constants/componentAtlases.ts
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Expand Up @@ -3,7 +3,7 @@ import { buildAtlas } from "../utils/atlases";
import { UCSC_CELL_BROWSER } from "./analysisPortals";

const NORMAL = "normal";
const TODO = "TODO";
const TODO = "--";

export const COMPONENT_ATLASES: Record<string, IntegratedAtlasRow[]> = {
adipose: [],
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340 changes: 339 additions & 1 deletion constants/datasets.ts
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Expand Up @@ -105,7 +105,345 @@ export const DATASETS = {
musculoskeletal: [],
"nervous-system": [],
oral: [],
organoid: [],
"organoid-neural": [
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids",
{
doi: "10.1038/s41380-020-0844-z",
officialHcaPublication: null,
publicationTitle:
"Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids",
publicationUrl: "https://doi.org/10.1038/s41380-020-0844-z",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids",
{
doi: "10.1016/j.stem.2018.12.015",
officialHcaPublication: null,
publicationTitle:
"hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids",
publicationUrl: "https://doi.org/10.1016/j.stem.2018.12.015",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Generation of Functional Human 3D Cortico-Motor Assembloids",
{
doi: "10.1016/j.cell.2020.11.017",
officialHcaPublication: null,
publicationTitle:
"Generation of Functional Human 3D Cortico-Motor Assembloids",
publicationUrl: "https://doi.org/10.1016/j.cell.2020.11.017",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells",
{
doi: "10.1038/s41587-020-00763-w",
officialHcaPublication: null,
publicationTitle:
"Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells",
publicationUrl: "https://doi.org/10.1038/s41587-020-00763-w",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets",
{
doi: "10.15252/embj.2022111118",
officialHcaPublication: null,
publicationTitle:
"Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets",
publicationUrl: "https://doi.org/10.15252/embj.2022111118",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Midbrain_organoid_Treutlein"
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex",
{
doi: "10.1016/j.cell.2022.09.010",
officialHcaPublication: null,
publicationTitle:
"Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex",
publicationUrl: "https://doi.org/10.1016/j.cell.2022.09.010",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Autism genes converge on asynchronous development of shared neuron classes",
{
doi: "10.1038/s41586-021-04358-6",
officialHcaPublication: null,
publicationTitle:
"Autism genes converge on asynchronous development of shared neuron classes",
publicationUrl: "https://doi.org/10.1038/s41586-021-04358-6",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells",
{
doi: "10.1016/j.stem.2021.04.006",
officialHcaPublication: null,
publicationTitle:
"Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells",
publicationUrl: "https://doi.org/10.1016/j.stem.2021.04.006",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Individual brain organoids reproducibly form cell diversity of the human cerebral cortex",
{
doi: "10.1038/s41586-019-1289-x",
officialHcaPublication: null,
publicationTitle:
"Individual brain organoids reproducibly form cell diversity of the human cerebral cortex",
publicationUrl: "https://doi.org/10.1038/s41586-019-1289-x",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells",
{
doi: "10.1016/j.neuron.2017.07.035",
officialHcaPublication: null,
publicationTitle:
"Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells",
publicationUrl: "https://doi.org/10.1016/j.neuron.2017.07.035",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Cell stress in cortical organoids impairs molecular subtype specification",
{
doi: "10.1038/s41586-020-1962-0",
officialHcaPublication: null,
publicationTitle:
"Cell stress in cortical organoids impairs molecular subtype specification",
publicationUrl: "https://doi.org/10.1038/s41586-020-1962-0",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures",
{
doi: "10.1038/s41593-018-0316-9",
officialHcaPublication: null,
publicationTitle:
"Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures",
publicationUrl: "https://doi.org/10.1038/s41593-018-0316-9",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Human CNS barrier-forming organoids with cerebrospinal fluid production",
{
doi: "10.1126/science.aaz5626",
officialHcaPublication: null,
publicationTitle:
"Human CNS barrier-forming organoids with cerebrospinal fluid production",
publicationUrl: "https://doi.org/10.1126/science.aaz5626",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Assembly of functionally integrated human forebrain spheroids",
{
doi: "10.1038/nature22330",
officialHcaPublication: null,
publicationTitle:
"Assembly of functionally integrated human forebrain spheroids",
publicationUrl: "https://doi.org/10.1038/nature22330",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Human cerebellar organoids with functional Purkinje cells",
{
doi: "10.1016/j.stem.2023.11.013",
officialHcaPublication: null,
publicationTitle:
"Human cerebellar organoids with functional Purkinje cells",
publicationUrl: "https://doi.org/10.1016/j.stem.2023.11.013",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation",
{
doi: "10.1016/j.stem.2020.02.002",
officialHcaPublication: null,
publicationTitle:
"Sliced Human Cortical Organoids for Modeling Distinct Cortical Layer Formation",
publicationUrl: "https://doi.org/10.1016/j.stem.2020.02.002",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development",
{
doi: "10.1016/j.stem.2019.08.002",
officialHcaPublication: null,
publicationTitle:
"Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development",
publicationUrl: "https://doi.org/10.1016/j.stem.2019.08.002",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Reliability of human cortical organoid generation",
{
doi: "10.1038/s41592-018-0255-0",
officialHcaPublication: null,
publicationTitle: "Reliability of human cortical organoid generation",
publicationUrl: "https://doi.org/10.1038/s41592-018-0255-0",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids",
{
doi: "10.1038/s41467-021-27464-5",
officialHcaPublication: null,
publicationTitle:
"Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids",
publicationUrl: "https://doi.org/10.1038/s41467-021-27464-5",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Inferring and perturbing cell fate regulomes in human brain organoids",
{
doi: "10.1038/s41586-022-05279-8",
officialHcaPublication: null,
publicationTitle:
"Inferring and perturbing cell fate regulomes in human brain organoids",
publicationUrl: "https://doi.org/10.1038/s41586-022-05279-8",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids",
{
doi: "10.1016/j.cell.2021.07.003",
officialHcaPublication: null,
publicationTitle:
"ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids",
publicationUrl: "https://doi.org/10.1016/j.cell.2021.07.003",
}
),
buildDataset(
[TODO],
0,
[TODO],
[TODO],
[TODO],
"Androgens increase excitatory neurogenic potential in human brain organoids",
{
doi: "10.1038/s41586-021-04330-4",
officialHcaPublication: null,
publicationTitle:
"Androgens increase excitatory neurogenic potential in human brain organoids",
publicationUrl: "https://doi.org/10.1038/s41586-021-04330-4",
}
),
],
pancreas: [],
reproduction: [],
skin: [],
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