|
| Status |
Public on Mar 19, 2020 |
| Title |
30292: microbial genes |
| Sample type |
SRA |
| |
|
| Source name |
Human nasal wash and throat sample
|
| Organism |
human metagenome |
| Characteristics |
tissue: Human nasal wash and throat sample
source: Human upper respiratory tract
ID: 30292
age: 21-36
Sex: Female
strain: H3N2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the human respiratory sample with the QIAGEN RNeasy Micro Kit
Double-stranded cDNA was synthesized and amplified from 200-500 picograms of input RNA with the NuGEN Ovation RNA-seq V2 kit and purified using the QIAquick PCR Purification Kit. cDNA was sheared to 250 bp using the S220 Focused-ultrasonicator and purified using Agencourt RNAClean XP beads. Sequencing libraries were prepared from 100 ng of purified, sheared cDNA with the NuGen Ovation Ultralow System V2 1-16. The libraries were sequenced on the Illumina HiSeq 2500 instrument with TruSeq SBS V3 chemistry according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Contaminating human, ribosomal RNA, and adaptor sequences were removed from each dataset using DeconSeq, SortMeRNA and Trimmomatic, respectively
The filtered reads were assigned to the orthologous gene families using the FMAP bioinformatics tool (FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies) and with the default KEGG-filtered Uniref90 reference cluster
The filtered reads were aligned to megares(antibiotic resistance database) by using BWA. The alignments were filtered that the genes need to be hit by at least two regions and at least 10 reads need to be assigned to the gene.
Supplementary_files_format_and_content: tab-delimited file with RPKM values for each gene feature and read counts for genes confer resistance to antibiotics
|
| |
|
| Submission date |
Feb 21, 2019 |
| Last update date |
Mar 19, 2020 |
| Contact name |
Elodie Ghedin |
| Organization name |
NYU
|
| Department |
Biology
|
| Lab |
Ghedin
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL26213 |
| Series (2) |
| GSE126901 |
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [RNA-Seq] |
| GSE126902 |
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection |
|
| Relations |
| BioSample |
SAMN10985106 |
| SRA |
SRX5405812 |
