|
| Status |
Public on Mar 26, 2024 |
| Title |
CD45+ brain leukocytes GEX 35595 |
| Sample type |
SRA |
| |
|
| Source name |
CD45+ enriched leukocytes
|
| Organism |
Macaca mulatta |
| Characteristics |
trim5: TFP/TFP
age (years.months): 17.8
Sex: F
cell type: CD45+ enriched leukocytes
treatment: Chronic SIV CL757 infection + ART (FTC/TDF/DTG)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated from brain derived live CD45+ and CD45- cells using the Chromium Nuclei Isolation Kit (10X Genomics) using manufacture instructions. Following isolation, nuclei were stored on ice and used immediately for subsequent library preparation.
Barcoded 3’ single cell gene expression library and ATAC library were prepared from single nuclei suspensions using the Chromium Single Cell Multiome kit (10X Genomics) following the manufacturer’s instruction. The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. The libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) with paired-end 150 bp reads with approximately 35,000 reads pairs per nuclei for gene expression and 25,000 read pairs per nuclei for ATAC libraries.
10X single nuclei multiome (snRNASeq and snATACSeq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
gene expression and chromatin accessible regions were generated using cellranger-arc (v2.0.2)
Assembly: Mmul_10
Supplementary files format and content: hdf5 binary files, gzipped tab delimited text files
|
| |
|
| Submission date |
Mar 19, 2024 |
| Last update date |
Sep 19, 2024 |
| Contact name |
Sonny Ramirez Elizaldi |
| E-mail(s) |
Srelizaldi@ucdavis.edu
|
| Organization name |
University of California Davis
|
| Department |
Immunology
|
| Lab |
Iyer Lab
|
| Street address |
County Road 98 and, Hutchison Dr
|
| City |
Woodland |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL27943 |
| Series (1) |
| GSE261968 |
Chromatin and gene expression profile at single nuclei level of CD45+ leukocytes from the rhesus brain parenchyma |
|
| Relations |
| BioSample |
SAMN40547773 |
| SRA |
SRX23995509 |
