title: HumanizedMice_ASDfeces-Caltech(Mazmanian)
design: mouse colon microbiome after colonization with human fecal samples from controls or ASD (V4 sequencing;  515F-806R). PowerSoil  DNA Isolation Kit (Mobio Carlsbard, CA) with a modification based on the manufacturer protocol. Quality and quantity of genomic DNA was verified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE). Qualified genomic DNA samples were processed for 16S rRNA library preparation and next-generation sequencing at the Microbiome Analysis Laboratory in the Biodesign Swette Center for Environmental Biotechnology (http://krajmalnik.environmentalbiotechnology.org/microbiome-lab.html). The Earth Microbiome Project standard protocols (http://www.earthmicrobiome.org/emp-standard-protocols/) were employed with the barcoded primer set 515F-806R (515F:GTGCCAGCMGCCGCGGTAA, 2086R:GGACTACHVGGGTWTCTAAT) that targets the V4 region of the bacterial (and archeal) 16S rRNA gene (Caporaso et al., 2012). Paired-end, 2x150bp, next-generation sequencing was performed using MiSeq Illumina platform (MiSeq Reagent Kit v2; Illumina Inc., San Diego, CA) and microbiome sequencing data were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME) software package (Caporaso et al., 2010)
library_name: 16S (V4) colon contents-humanizedMice_ASDfeces-Caltech(Mazmanian)-B761