Lung adenocarcinoma microbiome case-control study, Shanghai
120 samples from patients in Shanghai, China, examining bacterial, fungal and archaeal microbiome composition in relation to lung adenocarcinoma, using a case-control design. machine-written summary
120 samples · 120 runs · CN · Age unknown · 2024 · 23.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 840 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 22 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 120 | 100% | 120 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 120 | 100% | 120 | |||
| collection_date | 120 | 100% | 120 | |||
| detailed_location | 120 | 100% | ||||
| latitude | 120 | 100% | 120 | |||
| location_locality | 120 | 100% | 120 | |||
| location_region | 120 | 100% | 120 | |||
| longitude | 120 | 100% | 120 |
Archive description
This project aims to explore the landscape of microbiome (bacteria, fungi and archaea) in the patients with lung adenocarcinoma and to reveal the causal relationship between microbiome and tumorigenesis.
How this project entered the registry
Classified as human lower respiratory / gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host study.title · “Human lung cancer metagenomic raw sequence reads”
- body site run.scientific_name · “lung metagenome”
- body site sample.attr.isolation_source · “tumour tissue (n=50/120)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19030662 | collection_date | 2019-05-01/2019-08-01 | R1 | 0.90 | biosample.attribute:collection_date | 2019-05-01/2019-08-01 |
| SAMN19030662 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN19030662 | latitude | 31.3100 | R1 | 0.90 | biosample.attribute:lat_lon | 31.31 N 121.51 E |
| SAMN19030662 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN19030662 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.31 N 121.51 E |
| SAMN19030662 | longitude | 121.5100 | R1 | 0.90 | biosample.attribute:lat_lon | 31.31 N 121.51 E |
| SAMN19030662 | subject_id | patient 1 | R1 | 0.70 | sample.name_rule:library_names | patient 1_tissue_1 |
Sequencing
120 runs over 120 samples · mean 24.60 Gbp per run (median 23.80 Gbp, total 2,952.44 Gbp; 120 runs with a base count) · layout PAIRED 120 · platform ILLUMINA 120 · models Illumina NovaSeq 6000 (120) · 91% of runs with a Sandpiper profile · first public 2024-08-31
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA727667.csv.gz (3.9 KB) · parquet (74.3 KB) — all 120 samples, every field with route and confidence · PRJNA727667_determinations.csv.gz (6.7 KB) — 840 evidence rows