 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 13, 2023 |
| Title |
BM progenitor cells, HTO-derived cDNA [AsanoTag1] |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cKit+Lin- progenitor cells
tissue: bone marrow
library type: HTO
antibodies/tags: Naïve cMoP/TotalSeq-A961 ; Naïve GMP-MoP/TotalSeq-A962 ; Naïve cKit+Lin(CD90.2, CD19, NK1.1, SiglecF, Ly6G)- /TotalSeq-A963 ; LPS GMP-MoP/TotalSeq-A964 ; LPS cKit+Lin(CD90.2, CD19, NK1.1, SiglecF, Ly6G)-/TotalSeq-A965
|
| Extracted molecule |
protein |
| Extraction protocol |
BM cells from one naïve mouse and one LPS-injected mouse were sorted by FACSAriaIII and stained with different DNA barcode-conjugated PE-streptavidins (BioLegend Totalseq PE-streptavidin (A961, A962, A963, A964, and A965)) to identify each sample origin.
Sorted cells were pooled and subject to scRNA-seq using BD RhapsodyTM Single-Cell Analysis System (BD Biosciences), and resulted cDNA was amplified by TAS-Seq protocol. 100 cells /A961 ; 100 cells /A962 ; 15,000 cells /A963 ; 100 cells /A964 ; 15,000 cells /A965 were loaded onto BD RhapsodyTM Single-Cell Analysis System.
cDNA library was processed to sequencing library by using NEBNext UltraII FS library prep kit for Illumina (New England Biolabs).
Sequencing adapters were added to associated Totalseq PE-streptavidin libraries by PCR.
Pooled library concentration was adjusted to 2.0 nM and 12% PhiX control library v3 (Illumina) was spiked into the library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
|
| Data processing |
Each A961 and A963 or A964 and A965 datasets were integrated with merge functions of Seurat (version 4.2.0 in R version 4.2.1.).
Cells that contained a percentage of mitochondrial transcripts > 25% were filtered out.
PCA analysis was performed against 4777 of highly-variable genes identified by FindVariableFeatures (selection.method = mvp, mean.cutoff = c(0.1, Inf), dispersion.cutoff = c(0.5, Inf)) function in Seurat.
Naïve (A963) and LPS (A965) datasets were integrated with a combination of Find Integration Anchors and Integrate Data functions using rpca reduction.
1:52 PCs were selected by Jackstraw analysis and used for clustering analysis.
UMAP was performed on significant PCs for visualization in two dimensions.
Assembly: GRCm38 release 101
Supplementary files format and content: gene-expression matrix (.txt.gz)
|
| |
|
| Submission date |
Feb 07, 2023 |
| Last update date |
Mar 13, 2023 |
| Contact name |
Kenichi Asano |
| E-mail(s) |
asanok@toyaku.ac.jp
|
| Organization name |
Tokyo University of Pharmacy and Life Sciences
|
| Department |
Life Sciences
|
| Lab |
Immune Regulation
|
| Street address |
1432-1 Horinouchi
|
| City |
Hachioji |
| State/province |
Tokyo |
| ZIP/Postal code |
1920392 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE224701 |
GMP-MoPs can be classified as an independent cell type that differentiate from GMPs through proNeu1 without going through the MDP-cMoP pathway [scRNA-seq] |
| GSE224702 |
mouse RNA-seq, human RNA-seq, ATAC-seq, and scRNA-seq analyses data |
|
| Relations |
| BioSample |
SAMN33184237 |
| SRA |
SRX19301392 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7029811_Hashtag_top1M_AsanoTag1.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
