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

<p>&nbsp;</p><p>Datasets to go along with the publication listed:</p><p>full_object.rds: Brain Organoid Phospho-Seq dataset with ATAC, Protein and imputed RNA data</p><p>rna_object.rds: Reference whole cell scRNA-Seq object on Brain organoids</p><p>multiome_object.rds: Bridge dataset containing RNA and ATAC modalities for Brain organoids</p><p>metacell_allnorm.rds: Metacell object for finding gene-peak-protein linkages in Brain organoid dataset</p><p>fullobject_fragments.tsv.gz: fragment file to go with the full object</p><p>fullobject_fragments.tsv.gz.tbi:index file for the full object fragment file</p><p>multiome_fragments.tsv.gz: fragment file to go with the multiome&nbsp;object</p><p>multiome_fragments.tsv.gz.tbi:index file for the multiome object fragment file</p><p>K562_Stem.rds : object corresponding to the pilot experiment including K562 cells and iPS cells</p><p>K562_stem_fragments.tsv.gz:&nbsp; fragment file to go with the K562_stem object</p><p>K562_stem_fragments.tsv.gz.tbi: index file for the K562_stem object fragment file</p><p>retina.rds : object corresponding to the retinal organoid phospho-seq experiment</p><p>retina_fragments.tsv.gz:&nbsp; fragment file to go with the retina object</p><p>retina_fragments.tsv.gz.tbi: index file for the retina object fragment file</p><p>retina_multi.rds : object corresponding to the retinal organoid phospho-seq-multiome experiment</p><p>retina_multi_fragments.tsv.gz:&nbsp; fragment file to go with the retina_multi object</p><p>retina_multi_fragments.tsv.gz.tbi: index file for the retina_multi object fragment file</p><p>To use the K562, multiome,&nbsp;retina and retina_multiome datasets provided, please use these lines of code to import the object into Signac/Seurat&nbsp;and change the fragment&nbsp;file path to the corresponding downloaded fragment file:</p><p>obj &lt;- readRDS("obj.rds") # remove fragment file information Fragments(obj) &lt;- NULL # Update the path of the fragment file Fragments(obj) &lt;- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))</p><p>To use the K562 and multiome&nbsp;datasets provided, please use these lines of code to import the object into Signac/Seurat&nbsp;and change the fragment&nbsp;file path to the corresponding downloaded fragment file:</p><p>obj &lt;- readRDS("obj.rds") # remove fragment file information Fragments(obj) &lt;- NULL # Update the path of the fragment file Fragments(obj) &lt;- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))</p><p>To use the "fullobject" dataset&nbsp;provided, please use these lines of code to import the object into Signac/Seurat&nbsp;and change the fragment&nbsp;file path to the corresponding downloaded fragment file:&nbsp;</p><p>#load the stringr package library(stringr) #load the object obj &lt;- readRDS("obj.rds") # remove fragment file information Fragments(obj) &lt;- NULL #Remove unwanted residual information and rename cells obj@reductions$norm.adt.pca &lt;- NULL obj@reductions$norm.pca &lt;- NULL obj &lt;- RenameCells(obj, new.names = str_remove(Cells(obj), "atac_")) # Update the path of the fragment file Fragments(obj) &lt;- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))</p><p>&nbsp;</p><p>&nbsp;</p>