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GEO help: Mouse over screen elements for information. |
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Status |
Public on Dec 22, 2021 |
Title |
Single cell RNA sequencing of mouse brain hematopoietic cells after brain ischemia model |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We performed scRNA-seq of brain CD45+ hematopoietic cells from the brain of Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of middle cerebral artery occlusion (MCAO).
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Overall design |
Brain PI-CD45+ hematopoietic cells were sorted by flow cytometry from Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of MCAO. Three brains were pooled per each sample. Re-staining of PI of sorted samples were measured by flow cytometry, and the viability of all samples were more than 85%. Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics, PN-1000092) and the Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074) as per the manufacturer’s protocol. The sequencing of libraries was performed at Macrogen Japan (Kyoto, Japan) using an Illumina HiSeq X. Processed files were generated from Cell Ranger (10X Genomics) pipeline.
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Contributor(s) |
Kanemaru K, Oda C, Nakazawa Y, Abe F, Shibuya A |
Citation(s) |
34652960 |
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Submission date |
Jul 14, 2020 |
Last update date |
Dec 23, 2021 |
Contact name |
Akira Shibuya |
E-mail(s) |
ashibuya@md.tsukuba.ac.jp
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Organization name |
University of Tsukuba
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Department |
Immunology
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Lab |
Immunology
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Street address |
1-1-1 Tennodai
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City |
Tsukuba |
State/province |
Ibaraki |
ZIP/Postal code |
305-8575 |
Country |
Japan |
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Platforms (1) |
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Samples (6)
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GSM4670418 |
Brain CD45+ cells, Cd300a-fl/fl, naïve |
GSM4670419 |
Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, naïve |
GSM4670420 |
Brain CD45+ cells, Cd300a-fl/fl, 1 hr after MCAO |
GSM4670421 |
Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, 1 hr after MCAO |
GSM4670422 |
Brain CD45+ cells, Cd300a-fl/fl, 3 hr after MCAO |
GSM4670423 |
Brain CD45+ cells, Cd300a-fl/fl Lyz2-cre, 3 hr after MCAO |
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Relations |
BioProject |
PRJNA646185 |
SRA |
SRP271760 |
Supplementary file |
Size |
Download |
File type/resource |
GSE154396_RAW.tar |
352.6 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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