human gut metagenome
human gut biopsy from patient with late stage CRC
ENA first public
2024-10-28
External Id
SAMEA111529038
INSDC center name
Centre for Translational Microbiome Research (CTMR)
INSDC last update
2022-10-28T15:54:05Z
INSDC status
public
Submitter Id
long-indv257-normal
age_cat
2.70-74
altitude
0
ana_location
0.right colon
asa_cat
1.mild
associated_resource
processed based on https://doi.org/10.1101/286526
collection_date
2008
depth
26849.0
differentiation_grade
low
elev
105
env_broad_scale
environment associated with an animal part or small animal [ENVO:01001055]
env_local_scale
intestine environment [ENVO:2100002]
env_medium
intestine environment [ENVO:2100002]|intestinal epithelium [UBERON:0001277]|intestinal mucosaUBERON:0001242
gastrointest_disord
colorectal adenocarcinoma [DOID:0050861]
geo_loc_name
Sweden [GAZ:00002729]; Jonkoping County [GAZ:00003802]
host
Homo sapiens
host_age
70-74
host_body_mass_index
missing:not avaliable
host_body_product
biopsy [OBI:0002650]
host_body_site
right colon [UBERON:0008972]
host_body_temp
missing:not collected
host_diet
missing:not collected
host_disease_stat
colorectal adenocarcinoma [DOID:0050861]
host_subject_id
257
inhouse_name
1047
lat_lon
57.78 N 14.16 E
lib_layout
paired
long_survival
False
negative_cont_type
DNA-free PCR mix
nuc_acid_amp
https://doi.org/10.1101/286526 (1 step PCR)
nuc_acid_ext
https://doi.org/10.1101/286526
pcr_cond
initial denaturation:95C5min,98C_0.333min;annealing:51C_20s;elongation:72C_20s;final elongation:72C_1min;25
pcr_primers
FWD:CCTACGGGNGGCWGCAG;REV:GGACTACHVGGGTWTCTAAT
radical_micro
yes
radical_surgery
yes
samp_collec_device
biopsy
samp_collec_method
collected during resection for primary adenocarcinoma
sample name
long-indv257-normal
sample-id
long-indv257-normal
sample_name
1047
sample_size
missing: not collected
scientific_name
human gut metagenome
seq_meth
Illumina MiSeq [OBI: 0002003]
sex
female
short_survival
1
source_mat_id
1047
stage_tnm
stage IV
surgery_year
1.2006-2010
survival
long
target_gene
16S rRNA
target_subfragment
V34
tissue_num
0
tissue_type
normal
type_of_treatment_preop
none