|
| Status |
Public on Sep 19, 2016 |
| Title |
Volunteer 1 Winter |
| Sample type |
SRA |
| |
|
| Source name |
Anterior nare Sample
|
| Organism |
Staphylococcus aureus |
| Characteristics |
sequence events: 1
|
| Treatment protocol |
Stabilization of the RNA in the samples was performed by incubating with RNAprotect for 30 mins before proceeding with the RNA isolation.
|
| Growth protocol |
The in vivo samples were taken from the anterior nares of a human noses known to be an S. aureus carriers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
Amplification Protocol: Enriched mRNA fractions were amplified using the MessageAMP II-Bacteria RNA amplification according to manufacturer's instructions. Amplified samples were converted to ds-cDNA using SuperScript Double-Stranded cDNA Synthesis Kit and purified using GeneClean Turbo for PCR Kit (MP Biomed).
Paired-End DNA Sample Prep Kit (Illumina, San Diego, USA) according to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Human Nasal Community
|
| Data processing |
Illumina Base Calling: Libraries were sequenced on Illumina HiSeq2500 system with TrueSeq PE Cluster Kit V3 and TrueSeq SBSKit V3-HS (200cycles PE) Base calling were performed using the Illumina pipeline v 1.8.2
Filtering: Filtering and trimming with the following parameters: Q ≥ 15, Seq. length ≥ 90nt, Homopolymers ≤ 8nt and N's = 0.
Filtering: collapsing all the indexes from the machine into one file
human reads removal: Human reads were removed using BLAT against a human genome repository downloaded from NCBI ftp site. Sequences with >70% identity were removed
Ribosomal filtering: Ribosomal sequences were removed using HMMER (V3.0) using as a database models build with alignments of the Ribosomal fractions (5S,16S, and 23S) and BLASTN against a database of Ribosomal proteins of S. aureus genomes
S. aureus recruiting: Reads were recruited to S. aureus related via BLAST against 25 S. aureus genomes, reads with a ratio ≥ 80 (%id*AlnLength/QueryLength)
S. aureus mapping: Remaining reads were blasted (RPS-BLASTN) against a reference database of Position Scoring Matrices (PSM) build from a comparison of 25 Genomes of S. aureus
Down Sampling by Randomization: Read counts were down-sampled by a ramdom resampling using an in-house script written in perl
Normalization to counts per millon: Normalization to counts per millon
processed data files format and content: excel - abundance (by counting the number of transcripts) for each gene (groups of genes, OG) within each condition
Note: R2 reads weren't used for data processing
|
| |
|
| Submission date |
Sep 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Diego Chaves-Moreno |
| Organization name |
Helmholtz Centrum for Infection Research
|
| Department |
Department of Medical Microbiology (MMIK)
|
| Lab |
Research Group Microbial Interactions and Processes (MINP)
|
| Street address |
inhoffenstrasse 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19006 |
| Series (1) |
| GSE73485 |
Exploring the transcriptome of Staphylococcus aureus in its environmental niche |
|
| Relations |
| BioSample |
SAMN04115820 |
| SRA |
SRX1291978 |
