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| Status |
Public on Jan 30, 2023 |
| Title |
Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Viral respiratory infections are an important public health concern, due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious agent, including specific host immune responses, host genetic makeup and bacterial co-infections. To understand these interactions within natural infections we designed a longitudinal cohort study actively surveilling 18 different respiratory viruses over the course of 19 months (2016-2018) in Manhattan, New York City. The cohort includes individuals related to daycare facilities, high school students and health care workers. We retrieved weekly epidemiological and clinical data and collected over 4,000 nasal swabs for molecular characterization from 214 participants. Transcriptomic data enabled the characterization of specific markers of immune response, the identification of signatures associated with symptom severity and bacterial co-infections. We created a computational resource to facilitate access to the data and visualization of analytical results.
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| Overall design |
RNA-Seq, nasopharyngeal samples
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| Web link |
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002089#pbio-3002089-g002
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| Contributor(s) |
Galanti M, Patiño-Galindo JA, Filip I, Morita H, Galianese A, Natesan S, Youssef M, Comito D, Ligon C, Lane B, Matienzo N, Ibrahim S, Tagne E, Shittu A, Elliott O, Perea-Chamblee T, Scholes Rosenbloom D, Shaman J, Rabadan R |
| Citation(s) |
38236818 |
| Submission date |
Jan 25, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Angelica Galianese |
| E-mail(s) |
ag4555@cumc.columbia.edu
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| Organization name |
Columbia University
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| Street address |
615 W 164th Street, Apt 21C
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (847)
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| Relations |
| BioProject |
PRJNA927273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE223679_count_table_raw1.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw10.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw11.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw12.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw13.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw2.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw3.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw4.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw5.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw6.txt.gz |
322.1 Kb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw7.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
| GSE223679_count_table_raw9.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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