2024-10-28
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA111529126
External Id
Centre for Translational Microbiome Research (CTMR)
INSDC center name
2022-10-28T15:54:06Z
INSDC last update
public
INSDC status
ERS13639107
SRA accession
long-indv379-normal
Submitter Id
2.70-74
age_cat
0
altitude
2.rectum
ana_location
2.severe
asa_cat
processed based on https://doi.org/10.1101/286526
associated_resource
2012
collection_date
23635.0
depth
human gut biopsy from patient with late stage CRC
description
medium
differentiation_grade
105
elev
environment associated with an animal part or small animal [ENVO:01001055]
env_broad_scale
intestine environment [ENVO:2100002]
env_local_scale
intestine environment [ENVO:2100002]|intestinal epithelium [UBERON:0001277]|intestinal mucosaUBERON:0001242
env_medium
colorectal adenocarcinoma [DOID:0050861]
gastrointest_disord
Sweden [GAZ:00002729]; Jonkoping County [GAZ:00003802]
geo_loc_name
Homo spaiens
host
70-74
host_age
missing:not avaliable
host_body_mass_index
biopsy [OBI:0002650]
host_body_product
rectum [UBERON:0001052]
host_body_site
missing:not collected
host_body_temp
missing:not collected
host_diet
colorectal adenocarcinoma [DOID:0050861]
host_disease_stat
379
host_subject_id
1085
inhouse_name
57.78 14.16
lat_lon
paired
lib_layout
False
long_survival
DNA-free PCR mix
negative_cont_type
https://doi.org/10.1101/286526 (1 step PCR)
nuc_acid_amp
https://doi.org/10.1101/286526
nuc_acid_ext
human gut metagenome
organism
human gut metagenome
organism
initial denaturation:95C5min,98C_0.333min;annealing:51C_20s;elongation:72C_20s;final elongation:72C_1min;25
pcr_cond
FWD:CCTACGGGNGGCWGCAG;REV:GGACTACHVGGGTWTCTAAT
pcr_primers
yes
radical_micro
yes
radical_surgery
biopsy
samp_collec_device
collected during resection for primary adenocarcinoma
samp_collec_method
long-indv379-normal
sample-id
1085
sample_name
missing: not collected
sample_size
human gut metagenome
scientific_name
Illumina MiSeq [OBI: 0002003]
seq_meth
male
sex
1
short_survival
1085
source_mat_id
stage III
stage_tnm
2.2011-2017
surgery_year
long
survival
16S rRNA
target_gene
V34
target_subfragment
0
tissue_num
normal
tissue_type
radiation
type_of_treatment_preop