|
| Status |
Public on Jul 08, 2022 |
| Title |
C3-Cont-Tau |
| Sample type |
SRA |
| |
|
| Source name |
chimeric mouse brain cells with human microglia
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
treatment: Injected soluble tau from healthy human brain
|
| Treatment protocol |
PMPs were injected into P0 mouse brain using a digital sterotaxic device, human tau proteins were injected into each human microglial chimeric mouse at 2 months old.
|
| Growth protocol |
PMPs were generated from the three pairs of Cont and DS hiPSC cell lines using a previously established protocol (Haenseler et al., 2017). The yolk sac embryoid bodies (YS-EBs) were generated by treating the YS-EBs with mTeSR 1 media (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To stimulate myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). At 4-6 weeks after plating, human PMPs emerged into the supernatant and were continuously produced for more than 3 months. Human pNPCs were generated from Cont2 hiPSCs (Chen et al., 2016; Xu et al., 2019).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were collected after running dissociated cell through mouse cell removal column, RNA molecules were reverse transcriped and labeled with barcodes by folloing 10x Genomics' established protocol.
Libraries were constructed by folloing 10x Genomics' established protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scRNA-seq library
|
| Data processing |
The sequencing data was aligned with the pooled mouse (mm10, Ensembl 93) and human (hg19, Ensembl 87) reference genomes via Cell Ranger software.
Cells were summarized for all genes by species and those with >75% of reads aligning with hg19 were selected as human.
Raw hg19 counts from these cells were loaded into a new Seurat object, normalized and clustered.
Genome_build: hg19 + mm10
Supplementary_files_format_and_content: Processed Seurat object
|
| |
|
| Submission date |
Nov 19, 2021 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Mengmeng Jin |
| E-mail(s) |
mengmeng.jin@rutgers.edu
|
| Organization name |
Rutgers University
|
| Lab |
Jiang Lab
|
| Street address |
604 Allison Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (2) |
| GSE189226 |
Type I Interferon Signaling Mediates Microglial Dysfunction and Senescence in Human-Mouse Chimeric Brain Models of Down Syndrome and Alzheimer’s Disease [single-cell RNA-seq] |
| GSE189227 |
Type I Interferon Signaling Mediates Microglial Dysfunction and Senescence in Human-Mouse Chimeric Brain Models of Down Syndrome and Alzheimer’s Disease |
|
| Relations |
| BioSample |
SAMN23313480 |
| SRA |
SRX13180008 |
