title: unspecified sequencing; qiime_experiment_2223:1240473:54
design: A total of 100 samples, 25 each from burned and unburned soils, collected at both 4 (October 2010) and 16 weeks postfire (January 2011) were analyzed in this study. Soils were sampled roughly 1???m from the base of living (unburned) and dead (burned) tree trunks near the southeastern edge of the Fourmile Fire (40.039N, 105.391W), that was ignited on 6 September 2010 on the eastern slope of the Colorado Front Range, Boulder County, CO, USA.
library_construction_protocol: A fragment of the 16S rRNA gene encoding the V1-V2 region was amplified using modified primers of 27F and 338R adapted for Titanium chemistry (454 Life Sciences, Bradford, CT, USA). PCR reactions were performed in triplicate with 10????_l of sterile H2O, 10????_l of 5 PRIME hot master mix (5 PRIME, Gaithersburg, MD, USA), 2????_l (5????_M) of the reverse primer, 1????_l (10????_M) of the forward primer and 2????_l of the sample DNA. Samples were denatured for 3???min at 94?????C followed by 25 cycles at 94?????C for 45???s, 50?????C for 30???s, 72?????C for 90???s and a final elongation step at 70?????C for 10???min. Three replicate PCR products were quantified, pooled and cleaned using MO BIO UltraClean-htp PCR Clean-up kits and 16S rRNA gene amplicons were sent to the Environmental Genomics Core Facility (Engencore) at University of South Carolina for 454 Life Sciences GS FLX Titanium pyrosequencing.
attributes.tag: experiment_title
attributes.value: Nemergut_wildfire_soils
attributes.tag: target_subfragment
attributes.value: V2
attributes.tag: sample_center
attributes.value: CCME
attributes.tag: sequencing_meth
attributes.value: pyrosequencing
attributes.tag: experiment_center
attributes.value: CCME
attributes.tag: pcr_primers
attributes.value: FWD:TGCTGCCTCCCGTAGGAGT; REV:TCAGAGTTTGATCCTGGCTCAG
attributes.tag: run_center
attributes.value: Engencore
attributes.tag: num_sequences
attributes.value: 1661
attributes.tag: platform
attributes.value: Titanium
attributes.tag: library_construction_protocol
attributes.value: A fragment of the 16S rRNA gene encoding the V1-V2 region was amplified using modified primers of 27F and 338R adapted for Titanium chemistry (454 Life Sciences, Bradford, CT, USA). PCR reactions were performed in triplicate with 10????_l of sterile H2O, 10????_l of 5 PRIME hot master mix (5 PRIME, Gaithersburg, MD, USA), 2????_l (5????_M) of the reverse primer, 1????_l (10????_M) of the forward primer and 2????_l of the sample DNA. Samples were denatured for 3???min at 94?????C followed by 25 cycles at 94?????C for 45???s, 50?????C for 30???s, 72?????C for 90???s and a final elongation step at 70?????C for 10???min. Three replicate PCR products were quantified, pooled and cleaned using MO BIO UltraClean-htp PCR Clean-up kits and 16S rRNA gene amplicons were sent to the Environmental Genomics Core Facility (Engencore) at University of South Carolina for 454 Life Sciences GS FLX Titanium pyrosequencing.
attributes.tag: experiment_design_description
attributes.value: A total of 100 samples, 25 each from burned and unburned soils, collected at both 4 (October 2010) and 16 weeks postfire (January 2011) were analyzed in this study. Soils were sampled roughly 1???m from the base of living (unburned) and dead (burned) tree trunks near the southeastern edge of the Fourmile Fire (40.039N, 105.391W), that was ignited on 6 September 2010 on the eastern slope of the Colorado Front Range, Boulder County, CO, USA.
attributes.tag: row_number
attributes.value: 54
attributes.tag: target_gene
attributes.value: 16S rRNA
attributes.tag: study_center
attributes.value: CCME