Gut microbiome, metabolome in colon cancer, Shanghai
230 samples from Shanghai, China, comparing colorectal cancer (142) and healthy controls (88), analyzing microbiome, metabolome and host genomics to distinguish right- and left-sided colon cancer. machine-written summary
230 samples · 230 runs · CN · Age unknown · 2024 · 10.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,610 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 230 sample values (subject id) |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 210 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 | 230 | 100% | 230 | |||
| health_condition | 230 | 100% | 230 | |||
| subject_id | 230 | 100% | 230 | |||
| collection_date | 230 | 100% | 230 | |||
| detailed_location | 230 | 100% | ||||
| health_condition_detail | 230 | 100% | 230 | |||
| latitude | 230 | 100% | 230 | |||
| location_region | 230 | 100% | 230 | |||
| longitude | 230 | 100% | 230 |
Archive description
The distinct bacteria, metabolites and host genomics bring us a new dimension to define RCC and LCC
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human metagenome”
- body site study.title · “right- and left-sided colon cancer”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31901444 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN31901444 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shanghai |
| SAMN31901444 | health_condition | colorectal_cancer | R1 | 0.70 | sample.name_rule:sample_alias | CRC_1 |
| SAMN31901444 | health_condition_detail | CRC | R1 | 0.70 | sample.name_rule:sample_alias | CRC_1 |
| SAMN31901444 | latitude | 31.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 31 N 121 E |
| SAMN31901444 | location_region | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai |
| SAMN31901444 | longitude | 121.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 31 N 121 E |
| SAMN31901444 | subject_id | SAMN31901444 | R3 | 0.70 | design.one_sample_per_subject:fulltext | fecal samples from 230 preoperative patients with CRC and healthy controls were collected and detected by metagenomic sequencing |
Sequencing
230 runs over 230 samples · mean 10.85 Gbp per run (median 10.47 Gbp, total 2,496.65 Gbp; 230 runs with a base count) · layout PAIRED 230 · platform ILLUMINA 230 · models Illumina NovaSeq 6000 (230) · 91% of runs with a Sandpiper profile · first public 2024-01-01
Authors (0)
No author record.
Downloads
PRJNA888860.csv.gz (6.6 KB) · parquet (79.6 KB) — all 230 samples, every field with route and confidence · PRJNA888860_determinations.csv.gz (12.0 KB) — 1,840 evidence rows