friedue
commented
3 years ago However, I couldn't find marker gene list for neuron.
As described in the SingleR book: "The marker genes used for each label are reported in the metadata() of the SingleR() output." It's essentially this line of code:
all.markers <- metadata(predicted_labels)$de.genesI want to annotate more detailed for neuron subtype such as excitatory and inhibitory neurons. Is there any good reference to annotate?
I've used the Allan Brain Atlas data set in the past, you can check it out and see if your neurons of interest are part of it. The corresponding publication is Yao et al., 2021, I believe.
Here's some example code of how to turn the data that you can download here into a SingleCellExperiment object, which you can then use with SingleR using, for example, the subclass_label accessor. (SingleR details with scRNA-seq as a reference are part of the documentation).
library(data.table)
library(magrittr)
library(SingleCellExperiment)
library(Matrix)
gex <- fread("AllanBrainAtlas/SmartSeq/matrix.csv", sep = ",")
md <- fread("AllanBrainAtlas/SmartSeq/metadata.csv", sep = ",")
#"sample_name","donor_sex_label", "region_label", "subclass_label", "class_label"
#"class_color","neighborhood_label","neighborhood_color","outlier_call"
gex.mat <- as.matrix(gex[, -1])
rownames(gex.mat) <- gex$sample_name
# turn into sparse matrix
gex.mat <- as(gex.mat, "sparseMatrix")
gex.mat <- t(gex.mat)
cd <- DataFrame(md)
rownames(cd) <- cd$sample_name
cd$sample_name <- NULL
cd <- cd[colnames(gex.mat),]
sceall <- SingleCellExperiment(assays = list(counts = gex.mat),
colData = cd)
table(sceall$class_label)
#>GABAergic Glutamatergic Non-Neuronal
#> 22745 50002 1958
table(sceall$subclass_label)
# Astro CA1-ProS CA2 CA3
# 268 976 1701 21 315
# Car3 CR CT SUB DG Endo
# 1980 32 173 2469 213
# L2 IT ENTl L2 IT RHP L2/3 IT CTX-1 L2/3 IT CTX-2 L2/3 IT ENTl
# 179 375 5959 106 253
# L2/3 IT PPP L3 IT ENT L3 RSP-ACA L4/5 IT CTX L5 IT CTX
# 1395 577 200 11522 2934
# L5 IT TPE-ENT L5 NP CTX L5 PPP L5 PT CTX L6 CT CTX
# 338 2363 47 1974 6210
# L6 IT CTX L6 IT ENTl L6b CTX L6b/CT ENT Lamp5
# 5015 83 2213 693 4755
# Meis2 Micro-PVM NP PPP NP SUB Oligo
# 172 176 150 257 236
# Pvalb SMC-Peri Sncg Sst Sst Chodl
# 4365 198 1491 5258 268
# SUB-ProS V3d Vip VLMC
# 467 1 6436 159 If that's not suitable for your use-case, just turn to google.scholar to search for bulk or single-cell RNA-seq data sets you could use.
Hello!
I just have a question for annotation of "neuron". I've known that singleR uses various reference gene expression data to annotate accurately. In my data, most of cells were annotated in "Neurons". However, I couldn't find marker gene list for neuron.
I used "MouseRNAseqData()" function for reference.
Also, I want to annotate more detailed for neuron subtype such as excitatory and inhibitory neurons. Is there any good reference to annotate?
Always thank you for using nice tool!
Dahun