|
| Status |
Public on Dec 31, 2022 |
| Title |
Subject 061 VisitDay 084 Cohort IMRAS_Cohort 1_True Immunized |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Homo sapiens |
| Characteristics |
cohort: Cohort 1
subject: 61
tissue: Whole Blood
treatment: True Immunized
visit day: 84
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood samples taken from participants via venipuncture and collected into PaxGene tubes. Total RNA was extracted using PAXgene Blood Kit (PreAnalytiX) and globin mRNA removed using GLOBINclear Human Kit (Ambion).
RNA libraries were generated using standard manufacturers’ protocols for the two platforms (BGI’s BGIseq500 and Illumina’s HiSeq2000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
IMRAS061.084
processed data file: GEO_IMRAS_mapped_rawCounts.tsv
|
| Data processing |
a. Reads were aligned to the UCSC hg38 genome using Kallisto alignment tool.
b. Reads were quantified with RSEM.
c. Raw counts from two separate batches were combined into one matrix.
d. Original sample names used during processing were mapped to standardized sample names to include subjectId and visit day.
e. Four samples that could not be mapped to standardized subject-visit day format were excluded.
Genome_build: UCSC hg38 (GRCh38)
Supplementary_files_format_and_content: GEO_IMRAS_mapped_rawCounts.tsv: Tab-delimited file with raw counts for 265 samples.
|
| |
|
| Submission date |
Jul 03, 2018 |
| Last update date |
Jun 02, 2024 |
| Contact name |
Raphael Gottardo |
| Organization name |
Fred Hutch
|
| Department |
VIDD
|
| Lab |
Gottardo
|
| Street address |
1100 Fairview Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE192756 |
Phase 1 Trial With Challenge to Assess the Safety and Biomarkers of Protection in Malaria-naive Adults of Immunization Via Mosquito Bite With Radiation-Attenuated Plasmodium Falciparum Sporozoites (IMRAS) - Day 31-126 |
|
| Relations |
| BioSample |
SAMN09576804 |
| SRA |
SRX4339103 |
