Illumina HiSeq 2000 sequencing; qiita_ptid_64:1883.2010.241.Crump.Artic.LTREB.main.lane3.NoIndex
A 12-year sample archive of DNA from Alaskan arctic tundra ecosystems are available to the Earth Microbiome Project for comparison of microbial diversity across a range of arctic environments from soils to water to sediments. These samples were preserved and extracted using a method that differs from that of the EMP. Therefore, we must test how the extraction method used to extract our archived samples compares with those methods used by the EMP. The samples for this test were collected during the summer of 2011 at the Toolik Field Station. Each site was sampled in triplicate and samples were divided and preserved for extraction using our standard protocol (three replicates), and for extraction using the EMP protocol (three replicates). Half of the samples are from the epilimnion and hypolimnion of ultra-oligotrophic Toolik Lake collected over the course of the summer, and the rest are from different environments associated with a headwater stream that lies upslope of Toolik Lake. The data from these samples will allow us to test whether our extraction protocol yields results that are similar to the EMP extraction protocol, to investigate how replicates compare, and to determine how the microbial community and its metagenome changes over the course of the summer in Arctic tundra waters.
EMP V4 515f,806rbc protocol
barcode
AGCATGTCCCGT
center_name
CCME
center_project_name
Crump_Arctic_LTREB_main
emp_status
EMP
illumina_technology
HiSeq
linker
GT
pcr_primers
FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT
primer
GTGTGCCAGCMGCCGCGGTAA
run_center
CCME
run_date
2/1/14
run_prefix
Crump_Artic_LTREB_main_lane3_NoIndex
samp_size
0.1, gram
sample_center
University of Maryland
sequencing_meth
sequencing by synthesis
study_center
CCME
target_gene
16S rRNA
target_subfragment
V4