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| Status |
Public on May 01, 2024 |
| Title |
93T_Micro2,Rhesus Macauqe,12-days SIV infection,acute-infection |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Brain
cell type: CD11b and/or CD45 positive cells
treatment: 12-days SIV infection
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| Treatment protocol |
Three acute-infected rhesus macaques (93T, 94T, and 95T) were intravenously inoculated with SIVmac251
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the cryopreserved brains (104T, 111T) and fresh brains (92T, 93T, 94T, 95T). Isolates were immunomagnetically enriched for CD45+CD11b+ cells. The CD20 negative cells that were positive for either CD45 or CD11b or both CD45 and CD11b were collected for microglial/macrophages library preparations.
Post-sorting, isolates were concentrated to approximately 1000 cells per µL, and assessed by trypan blue for viability and concentration. Based on 10× Genomics parameters targeting 8000 cells, the ideal volume of cells was loaded onto the 10× Genomics (Pleasanton, CA, USA) Chromium GEM Chip and placed into the Chromium Controller for cell capturing and library preparation. This occurs through microfluidics and combining with Single Cell 3’ Gel Beads containing unique barcoded primers with a unique molecular identifier (UMI), followed by lysis of cells and barcoded reverse transcription of RNA, amplification of barcoded cDNA, fragmentation of cDNA to 200 bp, 5’ adapter attachment, and sample indexing as the manufacturer instructed with version 3 reagent kits. The prepared libraries were then sequenced using Illumina (San Diego, CA, USA) Nextseq550 and Novaseq6000 sequencers.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: Mmul10, NCBI RefSeq assembly and SIVmac251
Supplementary files format and content: FASTQ files contain the sequenced data
Supplementary files format and content: H5 files contain feature and cell barcode matrix
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| Submission date |
Jan 22, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Xiaoke Xu |
| E-mail(s) |
x.xu@unmc.edu
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| Organization name |
University of Nebraska Medical Center
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| Street address |
42nd and Emile
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| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198-7400 |
| Country |
USA |
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| Platform ID |
GPL29319 |
| Series (1) |
| GSE253835 |
Immunotyping of microglia and macrophages in the CNS during acute SIV infection: a single-cell study of rhesus macaque brains |
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| Relations |
| BioSample |
SAMN39529922 |
| SRA |
SRX23345899 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8028506_93T_Micro2_filtered_feature_bc_matrix.h5 |
26.7 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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