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))