 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2024 |
| Title |
4-RVz16 CD8 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph Node
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: Lymph Node
cell type: CD8
subject: RVz16
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cryopreserved LN samples from 5 A*01+ animals at D42 p.i. were thawed and stained with the following antibodies: anti-CD8-FITC (clone RPA-T8, BD Biosciences), anti-CD4-BV650 (clone OKT4, Biolegend), anti-Gag-PE (CM9 tetramer, NIH Tetramer Facility at Emory University, anti-CD95-PE/Cy7 (clone DX2, BD Biosciences), anti-CD28-APC (clone CD28.2, BD Biosciences), anti-CD3-APC/Cy7 (clone SP34-2, BD Biosciences). A minimum of 10,000 SIV-specific CD8 from each animal was sorted using a FACS Aria II system and loaded onto 10X Chromium Controller.
Single cells were partitioned into droplets (Gel Beads in Emulsion: GEMs) using Chromium NextGEM Single Cell 5’ Library & Gel Bead kits on the 10X Chromium Controller. The resulting cDNA was amplified and libraries were prepared for transcriptomic analysis according to manufacturer instructions. Gene expression libraries were sequenced as paired-end 26x91 reads on an Illumina NovaSeq6000 targeting a depth of 50,000 reads per cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Cell Ranger v3.1 software was used to perform demultiplexing of cellular transcript data, and mapping and annotation of UMIs and transcripts for downstream data analysis.
Assembly: Mmul10 from Ensembl release 100
Supplementary files format and content: H5 archive or cellbarcoded transcript counts
|
| |
|
| Submission date |
May 03, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL27943 |
| Series (1) |
| GSE266576 |
Distinct SIV-specific lymphoid tissue CD8 T cells exhibit simultaneous effector and stem-like profiles and associate with limited SIV persistence |
|
| Relations |
| BioSample |
SAMN41200020 |
| SRA |
SRX24450335 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8251944_4-RVz16_filtered_feature_bc_matrix.h5 |
6.0 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
