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| Status |
Public on May 01, 2024 |
| Title |
Liver innate immune cells, HTO-derived cDNA, lane 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: CD45.2+Lin (CD90.2, B220, NK1.1, SiglecF)-CD11b+ liver innate immune cells
genotype: Egr2fl/fl or Lyz2Cre/+.Egr2fl/fl
treatment: Normal diet or CDA-HFD
library type: HTO
antibodies/tags: Liver innate immune cells from ND-fed Egr2fl/fl mouse/TotalSeq-A951; Liver innate immune cells from ND-fed Lyz2Cre/+.Egr2fl/fl/TotalSeq-A952; Liver innate immune cells from CDA-HFD-fed Egr2fl/fl/TotalSeq-A953; Liver innate immune cells from CDA-HFD-fed Lyz2Cre/+.Egr2fl/fl /TotalSeq-A954
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| Extracted molecule |
protein |
| Extraction protocol |
Liver innate immune cells from ND-fed or CDA-HFD-fed WT and EGR2-KO mice were sorted by FACSAriaIII and stained with different DNA barcode-conjugated PE-streptavidins (BioLegend Totalseq PE-streptavidin (A951, A952, A953, and A954)) to identify each sample origin.
Sorted cells were pooled and subject to scRNA-seq using BD RhapsodyTM Single-Cell Analysis System (BD Biosciences), and resultant cDNA was amplified by TAS-Seq protocol. 3,000 cells /A951 ; 3,000 cells /A952 ; 9,000 cells /A953 ; 9,000 cells /A964 were loaded onto BD RhapsodyTM Single-Cell Analysis System.
cDNA library was processed into a sequencing library by using an NEBNext Ultra II FS DNA 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.
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| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
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| Data processing |
A951, A952,A953 and A964 datasets were integrated with merge functions of Seurat (version 4.1.1 in R version 4.2.1.).
Cells that contained more than 25% of mitochondrial transcripts were filtered out.
PCA analysis was performed against 5054 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.
1:57 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)
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| Submission date |
Apr 15, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Kenichi Asano |
| E-mail(s) |
asanok@toyaku.ac.jp
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| Organization name |
Tokyo University of Pharmacy and Life Sciences
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| Department |
Life Sciences
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| Lab |
Immune Regulation
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| Street address |
1432-1 Horinouchi
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| City |
Hachioji |
| State/province |
Tokyo |
| ZIP/Postal code |
1920392 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE263970 |
EGR2 biases the differentiation of liver infiltrating monocytes into hLAMs. |
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| Relations |
| BioSample |
SAMN40978028 |
| SRA |
SRX24269703 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8208194_Hashtag_top1M_AsanoTag2.txt.gz |
4.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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