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| Status |
Public on Dec 19, 2023 |
| Title |
DU09-03S0000039_L2 |
| Sample type |
SRA |
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| Source name |
whole blood
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| Organism |
Homo sapiens |
| Characteristics |
sequencing batch: 1
gender: female
age: 25
race: Black/African_American
site: United_States
infection type: Viral
pathogen: RespVirus_other
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole blood collected and stored at -80°C in PAXgene Blood RNA tubes using the PAXgene miRNA Extraction Kit
For batch 1, libraries were constructed using GlobinClear Globin RNA Reduction (Invitrogen) with TruSeq Stranded mRNA Library Kit (Illumina). For batch 2, libraries were contructed using NuGEN Universal Plus mRNA-Seq Library Prep Kit with AnyDeplete Globin depletion (NuGEN/Tecan).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Batch 1 was sequenced on an Illumina HiSeq 2500, and batch 2 was sequenced on an Illumina NovaSeq 6000.
For batch 1, adapters were removed by EA Genomics prior to receipt of sequences. For batch 2, adapters were remvoed using Trimmomatic v0.38.
Reads were aligned to the hg38 reference transcriptome using Bowtie2 with "option --very-sensitive-local"
Express version 1.5.1 was used for quantification at the transcript level. For batch 1 the option "strand rf-stranded" was used, and for batch 2 "strand fr-stranded" was used.
Expression data were normalized using the trimmed mean of M-values approach, specifically using the calcNormFactors function in the edgeR package in R.
Supplementary files format and content: The processed data file contains log2-transformed and normalized counts per million.
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| Submission date |
Aug 18, 2022 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Emily R. Ko |
| E-mail(s) |
[email protected]
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| Organization name |
Duke University
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| Department |
Medicine
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| Street address |
4103 Graceview Way
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27705 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE211567 |
Host-response Transcriptional Biomarkers Accurately Discriminate Bacterial and Viral Infections by Global Pathogens |
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| Relations |
| BioSample |
SAMN30397445 |
| SRA |
SRX17143086 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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