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Series GSE154396 Query DataSets for GSE154396
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
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).
 
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.
 
Contributor(s) Kanemaru K, Oda C, Nakazawa Y, Abe F, Shibuya A
Citation(s) 34652960
Submission date Jul 14, 2020
Last update date Dec 23, 2021
Contact name Akira Shibuya
E-mail(s) ashibuya@md.tsukuba.ac.jp
Organization name University of Tsukuba
Department Immunology
Lab Immunology
Street address 1-1-1 Tennodai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8575
Country Japan
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (6)
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
Relations
BioProject PRJNA646185
SRA SRP271760

Download family Format
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Supplementary file Size Download File type/resource
GSE154396_RAW.tar 352.6 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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