qiime_experiment_939:441259:16
qiime_experiment_939:441259:16
Case/Control comparison between infants with and without current wheezing episodes that live in the rural tropics of Ecuador
A29:16
Quadruplicated PCR products were pooled in 1 per sample, then were cleaned using AMPure XP bead kit and quantified using the Invitrogen Quant iT kit. Number of molecules were calculated per sample according to the Roche Junior 454 titanium Lib-L preparation manual, and the same amount of DNA molecules were multiplexed prior pyrosequencing. A ratio of 0.3 molecules of DNA per bead was used for the emPCR.
CCME-COLORADO
qiime_experiment_939:441259:16
experiment_center
NHLI_IMPERIAL_COLLEGE_LONDON
run_center
MOLECULAR GENETICS GROUP - NHLI
chimera_check
chimera slayer
target_gene
16S rRNA
sequencing_meth
pyrosequencing
run_date
10/28/10
pcr_primers
FWD:CCTACGGGAGGCAGCAG;REV:CCGTCAATTCMTTTRAGT
platform
FASTA
library_construction_protocol
Quadruplicated PCR products were pooled in 1 per sample, then were cleaned using AMPure XP bead kit and quantified using the Invitrogen Quant iT kit. Number of molecules were calculated per sample according to the Roche Junior 454 titanium Lib-L preparation manual, and the same amount of DNA molecules were multiplexed prior pyrosequencing. A ratio of 0.3 molecules of DNA per bead was used for the emPCR.
experiment_design_description
Case/Control comparison between infants with and without current wheezing episodes that live in the rural tropics of Ecuador
study_center
NHLI_IMPERIAL_COLLEGE_LONDON
library_selection
PCR
row_number
16
sample_center
FEPIS_QUININDE
pcr_cond
initial denaturation:94degC_2min; 30cycles of: denaturation=94degC_20sec; annealing=50degC_30sec; amplification=72degC_5min; final hold=4degC
nucl_acid_amp
Polymerase chain reaction (PCR) was used to amplify the variable regions 3 to 5 (V3-V5, Primers 454B_357F and 454A_926R 22) of the gene that encodes for 16S rRNA in bacteria.  Samples were multiplexed using sample specific barcodes23 and Roche 454 adaptor sequences (Roche Diagnostics, Oakland). To minimize PCR nucleotide insertion mistakes, a high fidelity Taq polymerase was used, and samples were amplified in quadruplicate reactions with 35 cycles each and then pooled.
key_seq
TCAG
experiment_title
Upper Airways Microbiota in Wheezing and Healthy Infants from the Tropics of Rural Ecuador
target_subfragment
V35
region
1
multiplex_ident
MID54
nucl_acid_ext
PMID: 20052433