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| Status |
Public on Jul 01, 2024 |
| Title |
LN, alum, replicate 2 |
| Sample type |
SRA |
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| Source name |
Lymph node
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Lymph node
cell type: Live CD3lowCD8lowCD20low single cells
treatment: MD39 + alum
age: 3 - 4 years old
Sex: female
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| Extracted molecule |
total RNA |
| Extraction protocol |
The inguinal LNs of vaccinated macaques were isolated 48 hours post-immunization. The collected lymph nodes were mechanically dissociated into a single cell suspension. Cells were filtered, counted, and resuspended in freezing medium before storage in liquid nitrogen and at -120C for subsequent analysis by single cell RNA sequencing.
Library construction was perfomed according to the manufacture's instruction (single cell 5` v2 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, and gene counting were done using the 10x Genomics Clound Analysis with the Cell Ranger Count v7.1.0
Assembly: Mmul_10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 23, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Darrell J. Irvine |
| E-mail(s) |
djirvine@mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE264685 |
scRNA-seq profiling of lymph node activation in non-human primate Rhesus macaques by aluminum hydroxide and saponin adjuvant SMNP |
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| Relations |
| BioSample |
SAMN41063583 |
| SRA |
SRX24349373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8226114_alum_rep2_barcodes.tsv.gz |
1.7 Mb |
(ftp)(http) |
TSV |
| GSM8226114_alum_rep2_features.tsv.gz |
164.5 Kb |
(ftp)(http) |
TSV |
| GSM8226114_alum_rep2_matrix.mtx.gz |
74.5 Mb |
(ftp)(http) |
MTX |
| GSM8226114_alum_rep2_seurat.RDS.gz |
231.5 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
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