833.California.HC24; Suchodolski_dog_ibd
IBD2_California_HC24_C5_R.K.1.20.12
ENA first public
2016-08-02
ENA last update
2016-06-02
External Id
SAMEA3924472
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
2016-06-02T18:38:05Z
INSDC status
public
Submitter Id
qiita_sid_833:833.California.HC24
age
1.5
age group
1.0
age unit
years
altitude
0
anonymized name
California.HC24
antibiotics
definite_no
assigned_from_geo
False
barcodesequence
CCTGCGAAGTAT
bcs
5.0
bcs_grouping
1_4
body habitat
UBERON:feces
body product
UBERON:feces
body site
UBERON:feces
breed
Parson_Jack_Russel_Terrier
breed_grouping
Terrier
collection date
1/30/12
collection_timestamp
1/30/12
common name
gut metagenome
country
USA: GAZ
crude_fiber_1000kcalg_me_group
1_10
depth
0
dewormed
True
disease_stat
healthy
dna_extracted
True
elevation
144.85
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.
g_fat_1000kcal_me_group
36_50
g_protein_1000kcal_me_group
62_85
gender_specific
FS
has_extracted_data
True
has_physical_specimen
True
host common name
domestic dog
host scientific name
Canis lupus familiaris
host subject id
California.HC24
host taxid
9615
illumina_technology
HiSeq
indiv_g_fat_1000kcal_me_group
92.2
indiv_g_protein_1000kcal_me_group
87.5
indoor_outdoor
indoor
latitude
36.78
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
-119.42
pcr primers
FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT
perc_crude_protein_min_group
26_35
percent_crude_fat_min_group
14_20
percent_crude_fiber_max_group
1_5
percent_met_cal_carb_group
10_37
percent_met_cal_fat_group
25_35
percent_met_cal_protein_group
27_38
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
2
protein source
chicken
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.California.HC24
sample_plate
IBD2
sequencing_meth
sequencing by synthesis
sex
female
size_grouping
small
state
California
state_us
California
study center
Texas A&M
target gene
16S rRNA
target subfragment
V4
tot_mass
5.4
travel_history
False
weight kg
5.4
weight_group
1.0
well id
C5