 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2024 |
| Title |
Animal_DCGM_W4_D0 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: PBMC
treatment: R21+3M-052-Alum
animal: DCGM
week: W4
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 |
DCGM_W4B
|
| 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 |
SAMN38752296 |
| SRA |
SRX22846445 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
