2 Import scRNA-seq plates
##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
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## intersect, setdiff, setequal, union## initializing scdb to scrna_db/2.0.1 Import Tet TKO chimera plates into metacell
This notebook requires that the UMI tables for each plate are available in the folder data/umi.tables . If they are not available, please run the cell below to download the necessary data
# If you need to download the umi tables, please run the two lines below
if (0) {
source("../scripts/download_data.R")
download_umi_tables()
}mat_nm <- "tko_chim"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "TKO"
treatment <- c("Chimera assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
# remove additionally the plate 190730_P03. No embryo and facs data available. Only relevant for TKO Chimera
metadata <- metadata[metadata$plate != "190730_P03", ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read 190303_P02## will read 190318_P01## will read 190318_P02## will read 190318_P03## will read 190318_P04## will read 190318_P05## will read 190318_P06## will read 190318_P07## will read 190318_P09## will read 190318_P11## will read 190318_P12## will read 190322_P01## will read 190322_P02## will read 190322_P04## will read 190325_P01## will read 190325_P02## will read 190325_P03## will read 190325_P04## will read 190325_P05## will read 190325_P07## will read 190325_P08## will read 190730_P01## will read 190730_P02## will read 190730_P04## will read 190730_P05## will read 190730_P06## will read 190730_P07## will read 190730_P08## will read 190730_P09## will read 190730_P10## will read 190730_P11## will read 190806_P04## will read 190806_P05## will read 190806_P06## will read 20190806_P01## will read 20190806_P02## will read 20190806_P03## will read 20190806_P07## will read 20190806_P08## will read 20190806_P09## will read 1106TKO29_01## will read 1106TKO29_02## will read 1106TKO29_03## will read 1106TKO29_04## will read 1106TKO29_05## will read 1106TKO29_06## will read 1106TKO29_07## will read 1106TKO29_08## will read 1106TKO29_09## will read 1106TKO29_10## will read 1106TKO29_11## will read 1106TKO29_12## will read 1106TKO29_13## will read 1106TKO29_14## will read 1106TKO29_15## will read 191108_P01## will read 191108_P02## will read 191108_P03## will read 191108_P04## will read 191108_P05## will read 191108_P06## will read 191108_P07## will read 191108_P08## will read 20200106_TKO26_P01_NOVA## will read 20200106_TKO26_P02_NOVA## will read 20200106_TKO26_P03_NOVA## will read 20200106_TKO26_P04_NOVA## will read 20200106_TKO26_P05_NOVA## will read TKO26_13_P01## will read TKO26_13_P02## will read TKO26_13_P03## will read TKO26_13_P04## will read TKO26_13_P05## will read TKO26_13_P06## will read TKO26_13_P07## will read TKO26_13_P08## will read TKO26_13_P09## will read TKO26_13_P10## will read TKO26_13_P11## will read TKO26_13_P12## will read TKO26_13_P15## will read TetTKO23_P01## will read TetTKO23_P02## will read TetTKO23_P03## will read TetTKO23_P04## will read TetTKO23_P05## will read TetTKO23_P06## will read TetTKO23_P07## will read TetTKO23_P08## will read TKO23_P01## will read TKO23_P02## will read TKO23_P04## will read TKO23_P05## will read TKO23_P06## [1] TRUE2.0.2 Import Tet TKO tetraploid-complemented embryos
mat_nm <- "tko_tetra"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "TKO"
treatment <- c("Tetraploid complementation assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read TKO26_tetra_191111_P01_NOVAseq## will read TKO26_tetra_191111_P02## will read TKO26_tetra_191111_P03## will read TKO26_tetra_191111_P04## will read 191125_P01_NOVA## will read 191125_P02## will read 191125_P03## will read 191125_P04## will read 4N_P01## will read 4N_P06## will read 4N26_01## will read 4N26_02## will read 4N26_03## will read 4N26_04## will read 4N26_05## will read 4N26_06## will read 4N26_07## will read 4N26_08## will read 4N_P07## will read 190819_P01## will read 190819_P02## will read 190819_P03## will read 190819_P04## will read 190916_P07## will read 190916_P08## will read 190916_P09## will read 4N_P04## will read 4N_P05## will read 4N_P08## will read 4N_P10## will read 4N_P11## will read 4N_P12## will read 4N_P13## will read 4N_P14## will read 4N29_01## will read 4N29_02## will read 4N29_03## will read 4N29_04## will read 4N29_05## will read 4N29_06## will read 4N29_07## will read 4N29_08## will read 4N29_09## will read 4N29_10## will read 4N29_11## will read 4N29_12## will read 4N29_13## will read 4N29_14## [1] TRUE# There are four mixed plates containing both tetraploid-complemented control and Tet TKO embryos
# We additionally ignore the cells from control embryos
mat <- scdb_mat("tko_tetra")
ctrl_cells <- mat@cell_metadata$cell[grep(pattern = "Ctrl", x = mat@cell_metadata$embryo)]
mat <- scm_ignore_cells(scmat = mat, ig_cells = union(mat@ignore_cells, ctrl_cells))
scdb_add_mat(id = "tko_tetra", mat = mat)2.0.3 Import Control tetraploid-complemented embryos
mat_nm <- "control_tetra"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "Control"
treatment <- c("Tetraploid complementation assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read 191125_P04## will read 190819_P01## will read 190916_P07## will read 190916_P09## will read 190916_P01## will read 190916_P02## will read 190916_P03## will read 190916_P04## will read 190916_P05## will read 190916_P06## will read 0217_P01## will read 0217_P02## will read 0217_P03## will read 0217_P04## will read 0217_P05## will read 191125_P05## will read 191125_P06_NOVA## will read 191125_P07## [1] TRUE# There are four mixed plates containing both tetraploid-complemented control and Tet TKO embryos
# We additionally ignore the cells from TKO embryos
mat <- scdb_mat("control_tetra")
tko_cells <- mat@cell_metadata$cell[grep(pattern = "TKO", x = mat@cell_metadata$embryo)]
length(tko_cells)## [1] 8092.0.4 Import Tet 1/2 DKO chimera embryos
mat_nm <- "dko12_chim"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "Tet1/2 DKO"
treatment <- c("Chimera assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read Tet12_0228_P01## will read Tet12_0228_P02## will read Tet12_0228_P03## will read Tet12_0228_P04## will read Tet12_0228_P05## will read Tet12_0228_P06## will read Tet12_0228_P07## will read Tet12_0228_P08## will read Tet12_0228_P09## will read Tet12_0228_P10## will read Tet12_0303_P01## will read Tet12_0303_P02## will read Tet12_0303_P03## will read Tet12_0303_P04## will read Tet12_1_0616## will read Tet12_2_0616## will read Tet12DKO_10## will read Tet12DKO_11## will read Tet12DKO_12## will read Tet12DKO_13## will read Tet12DKO_14## will read Tet12DKO_15## will read Tet12DKO_7## will read Tet12DKO_8## will read Tet12DKO_9## [1] TRUE2.0.5 Import Tet 1/3 DKO chimera embryos
mat_nm <- "dko13_chim"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "Tet1/3 DKO"
treatment <- c("Chimera assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read mTet13_P01## will read mTet13_P03## will read mTet13_P07## will read mTet13_P08## will read Tet13_0309_P02## will read Tet13_0309_P03## will read Tet13_0309_P04## will read Tet13_0309_P05## will read Tet13_2_0613## will read Tet13_DKO_3## will read Tet13_DKO_4## will read Tet13_P05## will read Tet13_P06## [1] TRUE2.0.6 Import Tet 2/3 DKO chimera embryos
mat_nm <- "dko23_chim"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "Tet2/3 DKO"
treatment <- c("Chimera assay")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read Tet23_0303_P01## will read Tet23_0303_P02## will read Tet23_0303_P03## will read Tet23_1## will read Tet23_2## will read Tet23_4## will read Tet23_5## will read Tet23_7## will read Tet23_8## will read Tet23_DKO_1_0616## will read Tet23_DKO_2_0616## will read Tet23DKO_3_0616## will read Tet23DKO_4_0616## [1] TRUE2.0.7 Import AAV-Cre delivered whole-embryo TKOs
mat_nm <- "tko_germline"
metadata <- read.csv(file = "data/plate_metadata.csv", stringsAsFactors = F)
genotype <- "TKO"
treatment <- c("AAV Cre-delivered Tet1/2/3 triple KO")
metadata <- metadata[metadata$treatment %in% treatment, ]
metadata <- metadata[grep(pattern = genotype, x = metadata$genotype), ]
import_plates(mat_nm = mat_nm, metadata = metadata)## will read TetAAV_P01## will read TetAAV_P07## will read TetAAV_P08## will read TetAAV_P10## will read TetAAV_P11## will read TetAAV_P12## will read TetAAV_P16## will read TetAAV_P18## will read TetAAV_P13_2## will read TetAAV_P19_2## [1] TRUE