Published November 16, 2023 | Version v2
Dataset Open

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

Description

 

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))

 

 

Files

Files (17.3 GB)

Name Size Download all
md5:7b78b9e4f7bb4c3cf5c4befd08f801dc
4.3 GB Download
md5:cee54fb101c38e005a110ceb7dbbe959
1.4 GB Download
md5:5ea276e66d49583f4dba6705875250eb
872.7 kB Download
md5:586eff217c85cb58238065161880b7a9
969.1 MB Download
md5:35aa02a42d0c803fb07131e461768df3
1.5 GB Download
md5:cb565a297c29111231c99149ae6b4565
919.9 kB Download
md5:e4c297d46c6d74e554626dac82917acd
393.3 MB Download
md5:39306a909f06b68ffd9c4b3c9f9b884c
825.6 kB Download
md5:ecba9bde69928c869ec69147be89a9e2
1.4 GB Download
md5:aff343ceca8213d48be073d68a7872e9
1.2 GB Download
md5:4ec41006003210492f61646afd76d719
3.3 GB Download
md5:70905516b359856e5b355534173014c4
1.2 GB Download
md5:b0d2bf0c00a21c61ae5664314d9841b6
825.1 kB Download
md5:af05306f8aa1e298e7ebf6f4a1804da1
564.2 MB Download
md5:62bbb46a928697680924e0f783c3ea2b
243.3 MB Download
md5:bdd53641efd0de77ef31a373989dd6ca
662.3 kB Download
md5:0ce2f65a9548e177ffb3dda18f02b039
930.7 MB Download