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PRJNA479838 SRP152675

Gut microbiota in colorectal adenoma patients, Nanning

human stool Raw sequence reads

Cross-sectional study of 35 stool samples from patients with colorectal adenomatous polyps in Nanning, China, examining intestinal flora diversity. machine-written summary

35 samples · 35 runs · CN · Age unknown · 2018 · 11.72 Gbp / sample

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Sources
✓Sequence archive 197○Abstract / description✓Full text 118✓Supplementary tables 112✓External resources 70–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive197 sample values (collection date, country, latitude, location locality, location region, longitude)
○ Abstract / descriptionread; no usable statement
✓ Full text118 sample values (antibiotic exposure, location region, location site, subject id) · PMC6930378
✓ Supplementary tables112 sample values (age, bmi, sex, smoking status)
✓ External resources70 sample values (health condition, health condition detail) · from GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult29
elderly6
Condition
colorectal_adenoma35
Sex
male20
female15
Country
CN35
Body site
primary35
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 4 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 31 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 11.72 Gbp per sample0130Gbp
Community composition
Phocaeicola 24.0%Bacteroides 17.5%Prevotella 15.3%Roseburia 3.9%Lachnospira 3.1%Alistipes 2.9%Faecalibacterium 2.3%Acetatifactor 1.9%Mediterraneibacter 1.7%Parabacteroides 1.4%Sutterella 1.1%Duodenibacillus 1.0%not assigned to a genus 2.3%other genera 21.6%

Genera, mean relative abundance over 33 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category35 100%
country35 100%35
health_condition35 100%35
subject_id35 100%35
age_at_collection_days35 100%35
antibiotic_exposure35 100%35
bmi35 100%35
collection_date35 100%35
detailed_location35 100%
health_condition_detail35 100%35
latitude35 100%35
location_locality35 100%35
location_region35 100%2213
location_site35 100%35
longitude35 100%35
sex35 100%35
smoking_status7 20%7
Papers (1)
  • Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps. 2020 PMID 31892851 PMC6930378 own_data
Details
Archive description

Intestinal flora diversity in patients with adenomatous polyps

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.

  • host study.title · “human stool Raw sequence reads”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN09605418age_at_collection_days25202R20.80paper.supp.ijbsv16p0135s2.xlsx[工作表1!age（year）]69
SAMN09605418antibiotic_exposurenoR30.70paper.body.methodsNo antibiotics were taken within two months
SAMN09605418bmi22.0R20.80paper.supp.ijbsv16p0135s2.xlsx[工作表1!BMI]22
SAMN09605418collection_date2017-11-06R10.90biosample.attribute:collection_date2017-11-06
SAMN09605418countryCNR10.90sample.attr.geo_loc_nameChina:Nanning
SAMN09605418health_conditioncolorectal_adenomaR20.75external.gmrepo sourcephenotype: Adenomatous Polyps
SAMN09605418health_condition_detailAdenomatous PolypsR20.75external.gmrepo sourcephenotype: Adenomatous Polyps
SAMN09605418latitude22.7900R10.90biosample.attribute:lat_lon22.79 N 108.34 E
SAMN09605418location_localityNanningR10.85biosample.attribute:geo_loc_nameChina:Nanning
SAMN09605418location_regionGuangxi Zhuangzu ZizhiquR10.60biosample.attribute:lat_lon22.79 N 108.34 E
SAMN09605424location_regionGuangxiR30.70paper.body.methodsLocal natives living in Guangxi for more than five years
SAMN09605418location_siteFirst Affiliated Hospital of Guangxi Medical UniversityR30.70paper.body.methodswe enrolled 35 patients with adenomatous polyps in the First Affiliated Hospital of Guangxi Medical University
SAMN09605418longitude108.3400R10.90biosample.attribute:lat_lon22.79 N 108.34 E
SAMN09605418sexmaleR20.80paper.supp.ijbsv16p0135s2.xlsx[工作表1!gender]male
SAMN09605422smoking_statuscurrentR20.80paper.supp.ijbsv16p0135s2.xlsx[工作表1!smoking]yes
SAMN09605418subject_idSAMN09605418R30.70design.one_sample_per_subject:fulltextwe enrolled 35 patients with adenomatous polyps in the First Affiliated Hospital
Sequencing

35 runs over 35 samples · mean 11.70 Gbp per run (median 11.72 Gbp, total 409.58 Gbp; 35 runs with a base count) · layout PAIRED 35 · platform ILLUMINA 35 · models HiSeq X Ten (35) · 94% of runs with a Sandpiper profile · first public 2018-07-09

Authors (0)

No author record.

Downloads

PRJNA479838.csv.gz (2.5 KB) · parquet (74.2 KB) — all 35 samples, every field with route and confidence · PRJNA479838_determinations.csv.gz (5.9 KB) — 497 evidence rows

Samples (35 · every field this project has values for · hover a cell for its source)
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