|
| Status |
Public on Jan 01, 2020 |
| Title |
Week25_stimulated_DF16_IDLow |
| Sample type |
SRA |
| |
|
| Source name |
DF16_IDLow
|
| Organism |
Macaca mulatta |
| Characteristics |
time after bcg vaccination: Week 25
stimulation: PPD-Stimulated Cells
tissue: Bronchoalveolar Lavage
vaccination route: Intradermal
vaccination dose: 5x10e5 CFU
|
| Treatment protocol |
PPD-Stimulated == Tuberculin Protein Purified Derivative-Stimulated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
high-throughput single-cell mRNA sequencing by Seq-Well was performed on single-cell suspensions obtain from NHP BAL. 15,000 vialble cells per sample were applied directly to the surface of a Seq-Well device. At each time point after BCG, 2 arrays were run for each sample - one unstimulated and one stimulated overnight with 20 ug/mL of PPD in R10.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Transcriptome of single cells
|
| Data processing |
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
Read 1 contains the barcode (bp 1-12) and UMI (13-18); Read 2 contains the biological sequence.
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: mmul_8.0.1
Supplementary_files_format_and_content: Filtered UMI-collapsed Matrix
|
| |
|
| Submission date |
Oct 30, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Alex Shalek |
| E-mail(s) |
[email protected]
|
| Organization name |
MIT
|
| Department |
Chemistry
|
| Lab |
Shalek Lab
|
| Street address |
45 Carleton Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL21120 |
| Series (1) |
| GSE139598 |
Prevention of Mycobacterium tuberculosis infection and disease in nonhuman primates following intravenous BCG vaccination |
|
| Relations |
| BioSample |
SAMN13159434 |
| SRA |
SRX7074024 |
