Suchodolski_dog_ibd; 833.Sweden.IBD.061A
IBD1_Sweden_IBD_061A_G9_R.K.1.20.12
ENA first public
2016-08-02
ENA last update
2016-06-02
External Id
SAMEA3924607
INSDC center alias
UCSDMI
INSDC center name
University of California San Diego Microbiome Initiative
INSDC first public
2016-08-02T17:03:04Z
INSDC last update
2016-06-02T18:38:08Z
INSDC status
public
Submitter Id
qiita_sid_833:833.Sweden.IBD.061A
age
6.7
age group
3.0
age unit
years
altitude
0
anonymized name
Sweden.IBD.061A
antibiotics
definite_no
assigned_from_geo
False
barcodesequence
TAGTATGCGCAA
body habitat
UBERON:feces
body product
UBERON:feces
body site
UBERON:feces
breed
Border_Terrier
breed_grouping
Terrier
collection date
1/30/12
collection_timestamp
1/30/12
common name
gut metagenome
country
Sweden: GAZ
depth
0
disease_stat
IBD
dna_extracted
True
elevation
13.02
emp status
NOT_EMP
env biome
ENVO:urban biome
env feature
ENVO:animal-associated habitat
env matter
ENVO:feces
experiment title
suchodolski_dog_ibd
experiment_center
Texas A&M
experiment_design_description
Fecal samples from dogs of various breeds, places of origin, and severity of bowel disorder were sequencing to obtain a dog gut metagenome.
gender_specific
M
has_extracted_data
True
has_physical_specimen
True
histo
large
host common name
domestic dog
host scientific name
Canis lupus familiaris
host subject id
Sweden.IBD.061A
host taxid
9615
illumina_technology
HiSeq
latitude
60.13
library construction protocol
This analysis was done as in Caporaso et al 2011 Genome research. The PCR primers F515 and R806 were developed against the V4 region of the 16S rRNA, both bacteria and archaea, which we determined would yield optimal community clustering with reads of this length The reverse PCR primer is barcoded with a 12-base error-correcting Golay code to facilitate multiplexing of up to 1,500 samples per lane, and both PCR primers contain sequencer adapter regions.
linker
GT
linkerprimersequence
GTGCCAGCMGCCGCGGTAA
longitude
18.64
pcr primers
FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT
physical_location
CCME
physical_specimen_location
Texas A&M
physical_specimen_remaining
False
platform
Illumina
platformchemistry
HiSeq_V4
pool name
R.K.1.20.12
primer_plate
1
public
False
required_sample_info_status
completed
run center
CCME
run date
1/30/12
run prefix
Suchodolski_dog_ibd
samp_size
0.1, gram
sample center
Texas A&M
sample name
qiita_sid_833:833.Sweden.IBD.061A
sample_plate
IBD1
sequencing_meth
sequencing by synthesis
sex
male
size_grouping
small
study center
Texas A&M
target gene
16S rRNA
target subfragment
V4
tot_mass
7.0
weight kg
7.0
weight_group
1.0
well id
G9