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Sample GSM7964618 Query DataSets for GSM7964618
Status Public on Jun 01, 2024
Title Animal_A15N125_W27_D0
Sample type SRA
 
Source name PBMC
Organism Macaca mulatta
Characteristics tissue: PBMC
treatment: R21+3M-052-Alum
animal: A15N125
week: W27
day: 0
group: 6
regimen: 0-8-24
Extracted molecule total RNA
Extraction protocol The blood Paxgene tubes were stored until all samples were collected. The whole blood samples were then subjected to RNA extraction using the Thermo Fisher “MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes.”
Sample QC was performed with Agilent 2100 bioanalyzer to identify samples with RIN > 7. Qualified RNA from each sample was processed with non-stranded mRNAseq library prep (with globin mRNA removal). In brief, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. Globin mRNA was depleted using globin mRNA probes. mRNA molecules were fragmented into small pieces using a fragmentation reagent, and the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. They were then end-repaired, followed by A-tailing and adapter ligation reactions. The library was subsequently PCR enriched and purified by the Ampure XP bead size selection method. All libraries are quantified by Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and paired-end 150-base reads were generated by sequencing using the sequencer G400.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description A15N125_W27B
Data processing Reads were aligned using STAR 2.7.10a
Assembly: Mmul-10
Supplementary files format and content: Reads per transcript, tab-delimited text
 
Submission date Dec 10, 2023
Last update date Jun 01, 2024
Contact name Dmitri A Kazmin
E-mail(s) dkazmin@stanford.edu
Organization name Stanford University
Department Institute for Immunity, Transplantation and Infection
Lab Bali Pulendran
Street address 240 Pasteur Dr
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platform ID GPL32224
Series (1)
GSE249806 Immunological assessment of multiple clinical-stage adjuvants to induce durable immune responses to the R21 malaria vaccine
Relations
BioSample SAMN38752444
SRA SRX22846481

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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