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

Datasets to go along with the publication listed:
full_object.rds: Brain Organoid Phospho-Seq dataset with ATAC, Protein and imputed RNA data
rna_object.rds: Reference whole cell scRNA-Seq object on Brain organoids
multiome_object.rds: Bridge dataset containing RNA and ATAC modalities for Brain organoids
metacell_allnorm.rds: Metacell object for finding gene-peak-protein linkages in Brain organoid dataset
fullobject_fragments.tsv.gz: fragment file to go with the full object
fullobject_fragments.tsv.gz.tbi:index file for the full object fragment file
multiome_fragments.tsv.gz: fragment file to go with the multiome object
multiome_fragments.tsv.gz.tbi:index file for the multiome object fragment file
K562_Stem.rds : object corresponding to the pilot experiment including K562 cells and iPS cells
K562_stem_fragments.tsv.gz:  fragment file to go with the K562_stem object
K562_stem_fragments.tsv.gz.tbi: index file for the K562_stem object fragment file
retina.rds : object corresponding to the retinal organoid phospho-seq experiment
retina_fragments.tsv.gz:  fragment file to go with the retina object
retina_fragments.tsv.gz.tbi: index file for the retina object fragment file
retina_multi.rds : object corresponding to the retinal organoid phospho-seq-multiome experiment
retina_multi_fragments.tsv.gz:  fragment file to go with the retina_multi object
retina_multi_fragments.tsv.gz.tbi: index file for the retina_multi object fragment file
To use the K562, multiome, retina and retina_multiome datasets provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file 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 multiome datasets provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file 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" dataset provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file 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))