 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 27, 2024 |
| Title |
Wastewater COVIDseq RUH 240327 PIR |
| Sample type |
SRA |
| |
|
| Source name |
wastewater
|
| Organism |
wastewater metagenome |
| Characteristics |
tissue: wastewater
sampling site: RUH
location type: WWTP
date: 240327
tna extraction_method: Promega Enviro TNA
inhibitor removal: yes
library preparation: Illumina COVIDseq
|
| Treatment protocol |
Following the operating instructions, the OneStepTM PCR inhibitor removal (PIR) kit (D6030, Zymo Research, Irvine, CA, USA) was used to remove inhibitors of molecular enzymatic reactions. The kit encompasses one cleaning step over a column, which efficiently retains inhibitors, including long and short chain humic acids, tannins or polyphenols. After column preparation, 100 µl aqueous TNA solution was transferred to the column and centrifuged for 3 min at 16,000 x g.
|
| Extracted molecule |
other |
| Extraction protocol |
Using the Wizard® Enviro TNA Kit (Promega Corp., Madison, USA) as a direct capture method, total nucleic acids (TNAs) were extracted and concentrated from 40 ml of 24 h composite samples, resulting in a final volume of 50-100 µl following the manufacturer’s instructions
Sequencing were prepared using the COVIDseq kit (Illumina) according to manufacturer's instructions, and sequenced on a NextSeq 2000 device using P1 300 cycles flowcells with 2x151 bp.
Targeted/amplicons
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Library name: COVIDseq_RUH_240327_mit_S8
|
| Data processing |
Sequencing on target reads and coverage are available in the processed data file. Additionally PCR results for SARS-CoV-2 are provided.
Assembly: Reads were mapped to SARS-CoV-2 via a bowtie2-samtools pipeline. Mapping only no assembly was performed.
Supplementary files format and content: CSV: Wastewater_COVIDseq_inhibitor_removal_processed_data.csv; Columns: "title","organism","sampling site","date","location type","treatment","inhibitor removal","on_target_alignment_rate","coverage","log10 SARS-CoV-2 copies per liter (PIR+D)"
|
| |
|
| Submission date |
Nov 27, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Emanuel Wyler |
| E-mail(s) |
[email protected]
|
| Phone |
+49 30 9406 3009
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Lab |
RNA Biology and Posttranscriptional Regulation
|
| Street address |
Robert Roessle Str 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL35141 |
| Series (1) |
| GSE283001 |
Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance |
|
| Relations |
| BioSample |
SAMN45079460 |
| SRA |
SRX26899099 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
