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feat: add organoid-brain to atlases page (#2443)
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Fran McDade authored and Fran McDade committed Sep 25, 2024
1 parent 37a7a47 commit f342b22
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Showing 8 changed files with 432 additions and 23 deletions.
2 changes: 1 addition & 1 deletion next/@types/network.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ export interface NetworkContext {

export interface AtlasModule {
Description: ElementType;
Inclusion: ElementType;
Inclusion?: ElementType;
}

export interface NetworkModule {
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8 changes: 6 additions & 2 deletions ...nts/HCABioNetworks/Network/Atlas/components/Overview/components/MainColumn/mainColumn.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ import { Table, Toolbar } from "../../../../../../../common/Table/table.styles";
import { SectionText } from "../../../../../../components/Section/section.styles";

export const MainColumn = (): JSX.Element => {
const { Description } = useAtlasContent();
const { Description } = useAtlasContent() || {};
const { atlas } = useAtlas();
const { integratedAtlases } = atlas;
return (
Expand All @@ -31,7 +31,11 @@ export const MainColumn = (): JSX.Element => {
<SectionContent>
<SectionTitle title="Atlas Description" />
<SectionText>
<Description />
{Description ? (
<Description />
) : (
"No atlas description available."
)}
</SectionText>
</SectionContent>
</Section>
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333 changes: 332 additions & 1 deletion next/constants/datasets.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,338 @@ export const DATASETS = {
musculoskeletal: [],
"nervous-system": [],
oral: [],
organoid: [],
"organoid-brain": [
buildDataset(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"Midbrain_organoid_Treutlein"
),
buildDataset(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"Cerebellar_organoid_Quadrato"
),
buildDataset(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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(
["--"],
0,
["--"],
["--"],
["--"],
"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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