Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells

DOI10.5281/zenodo.10120360Zenodo10120360MaRDI QIDQ6677976FDOQ6677976

Dataset published at Zenodo repository.

Philipp Wahle, Carol Dalgarno, Barbara Treutlein, John D Blair, Austin Hartman, Fides Zenk, Rahul Satija, Giovanna Brancati

Publication date: 16 November 2023

Copyright license: Creative Commons Attribution 4.0 International

Description

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))

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