|
| Status |
Public on Nov 11, 2012 |
| Title |
Environmental DNA form contaminated aquifer_Sep. 08_6.7m |
| Sample type |
SRA |
| |
|
| Source name |
Aquifer Sediment
|
| Organism |
aquifer metagenome |
| Characteristics |
sampling time: September 2008
depth: 6.7 m below ground
plume zone: Plume core
|
| Extracted molecule |
other |
| Extraction protocol |
Nucleic acids extracted with a bead beating-phenol/chloroform protocol from sediment samples were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads from 2 runs were furhter trimmed for quality and lenght (>250 bp).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
454 GS FLX |
| |
|
| Description |
small rDNA were amplified from total nucleic acids extracted from environmental samples using specific PCR primers
|
| Data processing |
Sequence data processing was performed using mothur, with binning of denoised and quality-trimmed sequences into operational taxonomic units (OTUs) at a 97% similarity cutoff.
|
| |
|
| Submission date |
Nov 15, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Pilloni |
| Organization name |
Helmholtz-Centre Munich
|
| Street address |
Ingolstädter Landstr. 1
|
| City |
Neuherberg |
| ZIP/Postal code |
85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26069 |
| Series (2) |
| GSE25345 |
High-throughput 16S rRNA amplicon pyrosequencing of contaminated aquifer sediment |
| GSE35631 |
Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes |
|
| Relations |
| SRA |
SRX031261 |
| BioSample |
SAMN00120419 |
