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| Status |
Public on Apr 04, 2023 |
| Title |
Rescue_mCherry_G19_2 |
| Sample type |
SRA |
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| Source name |
Mouse Human Chimera
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: striatal
cell line: G19
genotype: WT
transplant: Adult
animal: 1
phlorophore: mCherry
paradigm: HD Rescue
library: GOL2659A1
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were euthanized with euthasol, transcardially perfused with sterile Hank’s Balanced Salt Solution (HBSS) containing magnesium chloride and calcium chloride, and the brain removed. The brains were immersed in ice-cold sterile HBSS for about 5 minutes to facilitate the microdissection. Under a dissecting microscope, the striata from each mouse was dissected and placed in sterile HBSS on ice. The striatal tissues were transferred to a Petri dish containing sterile HBSS without magnesium chloride and calcium chloride, chopped into small pieces using sterile disposable scalpels, transferred into a sterile tube, and then incubated in a papain/DNase dissociation solution at 37°C for 50 minutes. Ovomuccoid dissolved in EBSS was then added to inactivate the papain. The tissue was triturated by repeated pipetting in order to achieve a single cell suspension. The cells were then pelleted, resuspended into MEM, and filtered for flow cytometry. Single cell suspensions were isolated based on their expression of mCherry, EGFP, or the lack of reporter expression on a BD FACSAria Fusion. To exclude dead cells, 4′,6-diamidino-2-phenylindole (DAPI) was added at 1 µg/mL.
Libraries were constructed according to the manufacturer instructions for the 10x chromium controller (v3.1 chemistry).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
scRNA-seq libraries were aligned with STARsolo (Kaminow et al., 2021) using a custom two-pass strategy. First, an annotated chimeric GRCh38 and GRCm38 reference was generated using Ensembl 102 human and mouse annotations with the addition of mCherry and EGFP. STARsolo was run with parameters: twopassMode = basic, limitSjdbInsertNsj = 3000000, and soloUMIfiltering = MultiGeneUMI. BAM files were then split by species and cross-species multimapping reads were assigned to both human or mouse BAMs. FASTQ files were re-generated from either the mouse or human BAM files andre-aligned to a single species reference.
Human data were imported into R using Seurat(Butler et al.,2018). Cells were filtered (Unique genes > 250 and percent mitochondrial genes < 15). Cells were then further filtered for appropriate expression of mCherry or EGFP. These filtered cells were used to construct the submitted processed data counts matices.
Assembly: GRCh38 and GRCm38 both with ensembl 102
Supplementary files format and content: Sparse (10x compatable) matrices containing filtered cells
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| Submission date |
Jun 16, 2022 |
| Last update date |
Apr 04, 2023 |
| Contact name |
Steven Goldman |
| Organization name |
University of Rochester Medical Center
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| Department |
Center for Translational Neuromedicine
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| Lab |
Goldman Lab
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| Street address |
601 Elmwood Ave
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platform ID |
GPL25526 |
| Series (1) |
| GSE206322 |
Young human glial progenitor cells outcompete and replace older and diseased human cells when transplanted into adult human glial chimeric mice |
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| Relations |
| BioSample |
SAMN29153417 |
| SRA |
SRX15765518 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6250586_Rescue_eGFP_G20_2.tar.gz |
1.1 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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