|
| Status |
Public on Jun 29, 2023 |
| Title |
Patient_25_D0_SEB |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood Mononuclear Cells
|
| Organism |
Homo sapiens |
| Characteristics |
subject: 25
time: D0
cell type: Peripheral Blood Mononuclear Cells
treatment: SEB
|
| 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 |
SAMN35738112 |
| SRA |
SRX20682605 |
