FASTQExperiment Detail
| Title | pyrosequencing-based analysis of 16S rRNA genes of sediments of South China Sea |
| Design Description | Bacterial 16s rRNA target at the V3 hypervariable region were amplified using a set of primers was designed by adding a 10-nucleotide barcode to the forward primer 8F (5?-AGAGTTTGATCCTGGCTCAG-3?) and reverse primer 533R (5?-TTACCGCGGCTGCTGGCAC-3?). |
| Organism | sediment metagenome |
Library Description
| Name | PCR AMPLICON |
| Strategy | AMPLICON |
| Source | METAGENOMIC |
| Selection | PCR |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 450 |
| Nominal Sdev | |
| Construction Protocol | Bacterial 16s rRNA target at the V3 hypervariable region were amplified using a set of primers was designed by adding a 10-nucleotide barcode to the forward primer 8F (5?-AGAGTTTGATCCTGGCTCAG-3?) and reverse primer 533R (5?-TTACCGCGGCTGCTGGCAC-3?). The amplification reaction mixture contained 5 Unit of Pfu Turbo DNA polymerase (Stratagene, La Jolla, CA, USA), and 1?Pfu reaction buffer, 200 ?M of dNTPs (TaKaRa, Dalin, China), 0.2?M barcoded primer and 20ng genomic DNA template in volume of 100 ?l. PCR was performed with a thermal cycler (Bio-Rad, USA) under the following condition: 5 min at 94?C, 25 cycles of 30 s at 94?C plus 45 s at 55?C plus 30 s at 72?C, and finally 5 min at 72?C. |
Platform
| Platform | LS454 |
| Instrument Model | 454 GS FLX |
Processing
| PipeSection | |
|---|---|
| Step Index | 1 |
| Prev Step Index | NIL |
| Program | |
| Version | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 0 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Technical Read |
| Read Type | BarCode |
| Base Coord | 1 |
| Read Index 1 | |
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 5 |
