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ERX1663831: Illumina HiSeq 2000 sequencing; qiita_ptid_44:1674.McG.F110714Jr1R4
1 ILLUMINA (Illumina HiSeq 2000) run: 24,714 spots, 3.7M bases, 2.2Mb downloads

Design: soil samples from parks and gardens in NY, NY
Submitted by: University of California San Diego Microbiome Initiative (University of California San Diego Microbiome Init)
Study: Urban stress is associated with variation in microbial species composition, but not richness, in Manhattan
show Abstracthide Abstract
Green roof and city park samples. In urban environments, green roofs provide a number of potential benefits, including decreases in urban heat island effects and reduced energy costs for buildings. However, they may also serve as habitat islands for maintaining biodiversity across the landscape, similarly to city parks. In this project, eleven experimental green roofs were sampled in addition to five city parks. The green roofs were spread across all five boroughs of New York City and were established in 2010 on top of select recreation centers run by the New York City Department of Parks and Recreation. All experimental green roofs were planted with the same density of native plant communities from the greater New York area and had identical soil substrate and planting box dimensions. The five city parks chosen for sampling included Central Park, the largest park in New York City, and the High Line, which is the newest large park established in the city. From each green roof, six composite soil cores (0-10 cm) were taken from six planting boxes (each box 4 m X 2 m) for a total of six representative samples per green roof. On three of the green roofs, we sampled in a spatially-explicit manner to capture fine-scale heterogeneity in microbial composition. For these samples, 10 individual soil cores were collected from three planting boxes for a total of 30 soil cores per roof. From each city park, three plots (20 m X 20 m) were sampled and five soil cores (0 to 10 cm) were composited as a representative sample for each plot. In Central Park, five plots were sampled rather than three plots due to the larger size of the park. Research questions: Do green roofs planted with native plants in New York City function as biodiversity reservoirs for bacteria, is there significant heterogeneity in microbial community composition at fine spatial scales within individual green roofs, based on the fine-scale spatial heterogeneity of green roof soil bacteria, how many samples are necessary to collect as a representative sample for each green roof, how much overlap is there in microbial community composition of the green roof substrates and city park soils and is there evidence for biogeographical structuring of green roof microbial communities across New York City.
Sample: Green roofs as biodiversity corridors in New York City; 1674.McG.F110714Jr1R4
SAMEA4392128 • ERS1303577 • All experiments • All runs
Organism: soil metagenome
Library:
Name: 1674.McG.F110714Jr1R4
Instrument: Illumina HiSeq 2000
Strategy: OTHER
Source: METAGENOMIC
Selection: PCR
Layout: SINGLE
Construction protocol: EMP V4 515f,806rbc protocol
Experiment attributes: (show all 17 attributes...) (hide...)
barcode: TAAGACTACTGG
center_name: ANL
center_project_name: Green roofs as biodiversity corridors in New York (show full text...)(hide...)
Green roofs as biodiversity corridors in New York City
emp_status: EMP
illumina_technology: MiSeq
linker: GT
pcr_primers: FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT
primer: GTGTGCCAGCMGCCGCGGTAA
run_center: ANL
run_date: 10/2/13
run_prefix: McGuire_S0_L001
samp_size: .1,g
sample_center: McGuire lab
sequencing_meth: sequencing by synthesis
study_center: CCME
target_gene: 16S rRNA
target_subfragment: V4
Runs: 1 run, 24,714 spots, 3.7M bases, 2.2Mb
Run# of Spots# of BasesSizePublished
ERR159333324,7143.7M2.2Mb2016-08-23

ID:
2946290

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