Gut & Oral Microbiome in Pancreatic Cancer, Kanazawa, Japan
57 fecal/saliva/tissue samples from pancreatic cancer patients and healthy controls in Kanazawa, Japan, analyzed by whole-genome sequencing in a case-control design. machine-written summary
57 samples · 57 runs · JP · Adult · 2020 · 0.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 456 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11487005, PMC8263681 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 57 | 100% | ||||
| country | 57 | 100% | 57 | |||
| health_condition | 57 | 100% | 57 | |||
| subject_id | 57 | 100% | 57 | |||
| collection_date | 57 | 100% | 57 | |||
| detailed_location | 57 | 100% | ||||
| health_condition_detail | 57 | 100% | 57 | |||
| latitude | 57 | 100% | 57 | |||
| location_locality | 57 | 100% | 57 | |||
| longitude | 57 | 100% | 57 |
- Dysbiotic gut microbiota in pancreatic cancer patients form correlation networks with the oral microbiota and prognostic factors. 2021 PMID 34249452 PMC8263681 own_data
- The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing. 2024 PMID 38874485 PMC11487005 unsure
Archive description
Fecal and salivary DNA collected from pancreatic cancer patients or healthy controls were sequenced by WGS
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “WGS of feces and saliva of”
- body site study.description · “Fecal and salivary DNA”
- body site study.title · “of feces and saliva of pancreatic cancer”
- body site study.description · “Fecal and salivary DNA collected from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16273809 | collection_date | 2014-06-30 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06-30 |
| SAMN16273809 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan: Kanazawa |
| SAMN16273809 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:source_material_id | HD07 |
| SAMN16273809 | health_condition_detail | HD | R1 | 0.70 | sample.name_rule:source_material_id | HD07 |
| SAMN16273809 | latitude | 36.5500 | R1 | 0.90 | biosample.attribute:lat_lon | 36.55 N 136.67 E |
| SAMN16273809 | location_locality | Kanazawa | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan: Kanazawa |
| SAMN16273809 | longitude | 136.6700 | R1 | 0.90 | biosample.attribute:lat_lon | 36.55 N 136.67 E |
| SAMN16273809 | subject_id | HD07 | R1 | 0.70 | sample.name_rule:source_material_id | HD07 |
Sequencing
57 runs over 57 samples · mean 0.53 Gbp per run (median 0.51 Gbp, total 30.32 Gbp; 57 runs with a base count) · layout PAIRED 52, SINGLE 5 · platform ILLUMINA 57 · models Illumina MiSeq (57) · 5% of runs with a Sandpiper profile · first public 2020-09-30 – 2020-10-01
Authors (49)
Matsukawa H first · Iida N · Kitamura K · Terashima T · Seishima J · Makino I · Kannon T · Hosomichi K · Yamashita T · Sakai Y · Honda M · Mizukoshi E · Kaneko S last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Merali N first · Chouari T · Sweeney C · Halle-Smith J · Jessel MD · Wang B · O' Brien J · Suyama S · Jiménez JI · Roberts KJ · Velliou E · Sivakumar S · Rockall TA · Demirkan A · Pedicord V · Deng D · Giovannetti E · Annels NE · Frampton AE last
Downloads
PRJNA665854.csv.gz (2.5 KB) · parquet (72.1 KB) — all 57 samples, every field with route and confidence · PRJNA665854_determinations.csv.gz (4.1 KB) — 456 evidence rows