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Sample GSM4144389 Query DataSets for GSM4144389
Status Public on Jan 01, 2020
Title Week13_stimulated_HBZ_IDLow
Sample type SRA
Source name HBZ_IDLow
Organism Macaca mulatta
Characteristics time after bcg vaccination: Week 13
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
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
BioSample SAMN13159403
SRA SRX7074022

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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