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Sample GSM3243960 Query DataSets for GSM3243960
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

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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