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Sample GSM7487537 Query DataSets for GSM7487537
Status Public on Jun 29, 2023
Title Patient_23_D90_Pfsz
Sample type SRA
 
Source name Peripheral Blood Mononuclear Cells
Organism Homo sapiens
Characteristics subject: 23
time: D90
cell type: Peripheral Blood Mononuclear Cells
treatment: P. falciparum schizonts
Treatment protocol Samples were stimulated with Plasmodium falciparum schizonts, or SEB, or were left unstimulated.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using QIAzol and the Direct-zol RNA Mini Prep Plus Kit per manufacturer's instructions. RNA quality was assessed using the Agilent Bioanalyzer 2100, and only samples with RNA integrity numbers (RIN) greater than 7 or total RNA concentration greater than 100 ng were selected for RNA sequencing racted using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
PolyA-enriched, strand-specific RNA libraries were constructed and 100bp paired-end reads were sequenced on an Illumina NovaSeq 6000 platform
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were assessed for quality, trimmed if PHRED scores fell below 20, and any remaining adapter sequences were removed
Processed paired-end reads were aligned to human reference genome GRCh38 using HISAT2, and counts were generated using the HTseq analysis package
Reads that successfully mapped to the reference genome were used for downstream analyses
Assembly: GRCh38
Supplementary files format and content: htseq output with gene counts for each sample
 
Submission date Jun 14, 2023
Last update date Jun 29, 2023
Contact name Carrie McCracken
E-mail(s) cmccracken@som.umaryland.edu
Organization name Institute of Genome
Department Institute for Genome Sciences
Street address 670 W. Baltimore St
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL24676
Series (1)
GSE234970 Immunogenomic profile at baseline predicts host susceptibility to clinical malaria
Relations
BioSample SAMN35738072
SRA SRX20682617

Supplementary file Size Download File type/resource
GSM7487537_IGS_MLI_0015rhd2c4.accepted_hits.sorted_by_name.exon.counts.txt.gz 47.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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