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

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))