Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells
收藏资源简介：
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))
本数据集配套如下已发表研究成果： - `full_object.rds`：包含脑类器官磷酸化测序（Phospho-Seq）、转座酶可及性测序（ATAC, Assay for Transposase-Accessible Chromatin sequencing）、蛋白质组及推定转录组（RNA）数据的数据集 - `rna_object.rds`：针对脑类器官的全细胞单细胞RNA测序（scRNA-Seq, single-cell RNA Sequencing）参考对象文件 - `multiome_object.rds`：涵盖脑类器官转录组（RNA）与转座酶可及性测序（ATAC）模态的桥接数据集 - `metacell_allnorm.rds`：用于在脑类器官数据集中挖掘基因-峰-蛋白质关联的元细胞（Metacell）对象文件 - `fullobject_fragments.tsv.gz`：配套完整对象的片段文件 - `fullobject_fragments.tsv.gz.tbi`：完整对象片段文件的索引文件 - `multiome_fragments.tsv.gz`：配套多组学对象的片段文件 - `multiome_fragments.tsv.gz.tbi`：多组学对象片段文件的索引文件 - `K562_Stem.rds`：对应包含K562细胞与诱导多能干细胞（iPS, induced Pluripotent Stem cells）的预实验对象文件 - `K562_stem_fragments.tsv.gz`：配套`K562_Stem`对象的片段文件 - `K562_stem_fragments.tsv.gz.tbi`：`K562_Stem`对象片段文件的索引文件 - `retina.rds`：对应视网膜类器官磷酸化测序实验的对象文件 - `retina_fragments.tsv.gz`：配套`retina`对象的片段文件 - `retina_fragments.tsv.gz.tbi`：`retina`对象片段文件的索引文件 - `retina_multi.rds`：对应视网膜类器官磷酸化测序-多组学联合实验的对象文件 - `retina_multi_fragments.tsv.gz`：配套`retina_multi`对象的片段文件 - `retina_multi_fragments.tsv.gz.tbi`：`retina_multi`对象片段文件的索引文件 若需使用本次提供的K562、多组学、视网膜及视网膜多组学数据集，请使用如下代码将对象导入Signac/Seurat分析环境，并将片段文件路径替换为对应下载的片段文件实际路径： r obj <- readRDS("obj.rds") # 移除原有片段文件信息 Fragments(obj) <- NULL # 更新片段文件路径 Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj)) 若需使用本次提供的K562与多组学数据集，请使用如下代码将对象导入Signac/Seurat分析环境，并将片段文件路径替换为对应下载的片段文件实际路径： r obj <- readRDS("obj.rds") # 移除原有片段文件信息 Fragments(obj) <- NULL # 更新片段文件路径 Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj)) 若需使用本次提供的`fullobject`数据集，请使用如下代码将对象导入Signac/Seurat分析环境，并将片段文件路径替换为对应下载的片段文件实际路径： r # 加载stringr工具包 library(stringr) # 加载目标对象 obj <- readRDS("obj.rds") # 移除原有片段文件信息 Fragments(obj) <- NULL # 移除冗余降维结果并重命名细胞 obj@reductions$norm.adt.pca <- NULL obj@reductions$norm.pca <- NULL obj <- RenameCells(obj, new.names = str_remove(Cells(obj), "atac_")) # 更新片段文件路径 Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))
