{"entities":{"Q6677976":{"pageid":14397284,"ns":120,"title":"Item:Q6677976","lastrevid":54755180,"modified":"2026-01-29T20:33:31Z","type":"item","id":"Q6677976","labels":{"en":{"language":"en","value":"Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells"}},"descriptions":{"en":{"language":"en","value":"Dataset published at Zenodo repository."}},"aliases":{},"claims":{"P31":[{"mainsnak":{"snaktype":"value","property":"P31","hash":"dae155fd0809a7906855cd4fa50dd7d71bed552b","datavalue":{"value":{"entity-type":"item","numeric-id":56885,"id":"Q56885"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$770E0827-085C-4F6F-B81B-DDBD9481A8C8","rank":"normal"}],"P1459":[{"mainsnak":{"snaktype":"value","property":"P1459","hash":"106872a57ac6e7e03e8ca010032b15d95d706757","datavalue":{"value":"Datasets to go along with the publication listed:full_object.rds: Brain Organoid Phospho-Seq dataset with ATAC, Protein and imputed RNA datarna_object.rds: Reference whole cell scRNA-Seq object on Brain organoidsmultiome_object.rds: Bridge dataset containing RNA and ATAC modalities for Brain organoidsmetacell_allnorm.rds: Metacell object for finding gene-peak-protein linkages in Brain organoid datasetfullobject_fragments.tsv.gz: fragment file to go with the full objectfullobject_fragments.tsv.gz.tbi:index file for the full object fragment filemultiome_fragments.tsv.gz: fragment file to go with the multiomeobjectmultiome_fragments.tsv.gz.tbi:index file for the multiome object fragment fileK562_Stem.rds : object corresponding to the pilot experiment including K562 cells and iPS cellsK562_stem_fragments.tsv.gz: fragment file to go with the K562_stem objectK562_stem_fragments.tsv.gz.tbi: index file for the K562_stem object fragment fileretina.rds : object corresponding to the retinal organoid phospho-seq experimentretina_fragments.tsv.gz: fragment file to go with the retina objectretina_fragments.tsv.gz.tbi: index file for the retina object fragment fileretina_multi.rds : object corresponding to the retinal organoid phospho-seq-multiome experimentretina_multi_fragments.tsv.gz: fragment file to go with the retina_multi objectretina_multi_fragments.tsv.gz.tbi: index file for the retina_multi object fragment fileTo use the K562, multiome,retina and retina_multiome datasets provided, please use these lines of code to import the object into Signac/Seuratand change the fragmentfile path to the corresponding downloaded fragment file:obj - readRDS(\"obj.rds\") # remove fragment file information Fragments(obj) - NULL # Update the path of the fragment file  Fragments(obj) - CreateFragmentObject(path = \"download/obj_fragments.tsv.gz\", cells = Cells(obj))To use the K562 and multiomedatasets provided, please use these lines of code to import the object into Signac/Seuratand change the fragmentfile path to the corresponding downloaded fragment file:obj - readRDS(\"obj.rds\") # remove fragment file information Fragments(obj) - NULL # Update the path of the fragment file Fragments(obj) - CreateFragmentObject(path = \"download/obj_fragments.tsv.gz\", cells = Cells(obj))To use the \"fullobject\" datasetprovided, please use these lines of code to import the object into Signac/Seuratand change the fragmentfile path to the corresponding downloaded fragment file:#load the stringr package library(stringr) #load the object obj - readRDS(\"obj.rds\") # remove fragment file information Fragments(obj) - NULL #Remove unwanted residual information and rename cells obj@reductions$norm.adt.pca - NULL obj@reductions$norm.pca - NULL obj - RenameCells(obj, new.names = str_remove(Cells(obj), \"atac_\")) # Update the path of the fragment file  Fragments(obj) - CreateFragmentObject(path = \"download/obj_fragments.tsv.gz\", cells = Cells(obj))","type":"string"},"datatype":"string"},"type":"statement","id":"Q6677976$3B400FF1-0BBE-4DA6-88BC-4D9A5FE86A63","rank":"normal"}],"P28":[{"mainsnak":{"snaktype":"value","property":"P28","hash":"ec3ecea5c09fc0c2fccf666e4f503b4f338e1922","datavalue":{"value":{"time":"+2023-11-16T00:00:00Z","timezone":0,"before":0,"after":0,"precision":11,"calendarmodel":"http://www.wikidata.org/entity/Q1985727"},"type":"time"},"datatype":"time"},"type":"statement","id":"Q6677976$39148E0C-E3C0-417A-8DDE-24DB8E153DC6","rank":"normal"}],"P16":[{"mainsnak":{"snaktype":"value","property":"P16","hash":"9447b319e6ace33d8ec3c7f8963960d2bfd74769","datavalue":{"value":{"entity-type":"item","numeric-id":6677970,"id":"Q6677970"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$4194B16C-AA1F-491C-8ACF-0B8794D4CC73","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"c054292e94e36b9df66c1f71da1e12b2b65797de","datavalue":{"value":{"entity-type":"item","numeric-id":5979949,"id":"Q5979949"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$637747B8-DE73-4EFB-BDFE-3C366965D14E","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"4317986a825ce3d5dbe8abb44f53c8025eb9b6c8","datavalue":{"value":{"entity-type":"item","numeric-id":6677971,"id":"Q6677971"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$668A66FB-CA96-4C7B-B315-7336C4DE20A7","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"80b77737862f7389cc1040a90f5cfcffd8f99628","datavalue":{"value":{"entity-type":"item","numeric-id":6677972,"id":"Q6677972"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$303F2456-5138-4DD7-AF80-4BA718B246BF","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"1e56eb756948d6abd5c82fda67ba8e379ec88878","datavalue":{"value":{"entity-type":"item","numeric-id":6677973,"id":"Q6677973"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$3EA8A6F4-479D-4713-8615-82EF1A0C48A0","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"212c19a68bdf3aad3e698efebd311156fad9176c","datavalue":{"value":{"entity-type":"item","numeric-id":85858,"id":"Q85858"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$7515E558-90BA-4851-A5D2-E5A8655149E5","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"71c44a4471caefbd73aa3dc6e7edf334599b0c21","datavalue":{"value":{"entity-type":"item","numeric-id":6677974,"id":"Q6677974"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$19ECB947-BFE5-464A-BC24-3690EC48CD10","rank":"normal"},{"mainsnak":{"snaktype":"value","property":"P16","hash":"2f3b5cb72776be9a7e90cae7c4a06f0347d78893","datavalue":{"value":{"entity-type":"item","numeric-id":6677975,"id":"Q6677975"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$E02BA34E-D4CA-4163-8121-CEA77F068D39","rank":"normal"}],"P227":[{"mainsnak":{"snaktype":"value","property":"P227","hash":"81662eaf1a9fd3fb81f18945ddb3d6247b93fc7e","datavalue":{"value":"10120360","type":"string"},"datatype":"external-id"},"type":"statement","id":"Q6677976$7512BD06-16C1-4D0B-811A-C4078339EB90","rank":"normal"}],"P27":[{"mainsnak":{"snaktype":"value","property":"P27","hash":"c0103adb64767a1576581d37926d39821930babe","datavalue":{"value":"10.5281/zenodo.10120360","type":"string"},"datatype":"external-id"},"type":"statement","id":"Q6677976$AABAAEAD-6E47-4CE4-9E73-0D5291D4EEA1","rank":"normal"}],"P163":[{"mainsnak":{"snaktype":"value","property":"P163","hash":"45fcd4163b5f33e6e8c784f5522d7246c0a1a61e","datavalue":{"value":{"entity-type":"item","numeric-id":57056,"id":"Q57056"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$5282C929-4001-4C20-A906-012E566385CD","rank":"normal"}],"P1460":[{"mainsnak":{"snaktype":"value","property":"P1460","hash":"d1e8073b72a070520efd3d14d4b3d2d3d03859e2","datavalue":{"value":{"entity-type":"item","numeric-id":5984635,"id":"Q5984635"},"type":"wikibase-entityid"},"datatype":"wikibase-item"},"type":"statement","id":"Q6677976$3497BEE1-2609-408D-8EB6-E386C5F20C11","rank":"normal"}]},"sitelinks":{"mardi":{"site":"mardi","title":"Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells","badges":[],"url":"https://portal.mardi4nfdi.de/wiki/Phospho-seq:_Integrated,_multi-modal_profiling_of_intracellular_protein_dynamics_in_single_cells"}}}}}