Mucosal virome & transcriptome in colorectal polyps
94 paired mucosal samples from colorectal polyp and adjacent normal tissue in Australia, profiled for virome and transcriptome using a case-control design. machine-written summary
94 samples · 94 runs · AU · Age unknown · 2025 · 10.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 618 sample values (collection date, country, health condition, health condition detail, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 94 sample values (location site) · PMC12439157 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
41 of 41 people sampled more than once (82 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 30 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 | 94 | 100% | 94 | |||
| health_condition | 80 | 85% | 80 | |||
| subject_id | 82 | 87% | 82 | |||
| collection_date | 94 | 100% | 94 | |||
| detailed_location | 94 | 100% | ||||
| latitude | 94 | 100% | 94 | |||
| location_site | 94 | 100% | 94 | |||
| longitude | 94 | 100% | 94 | |||
| health_condition_detail | 80 | 85% | 80 |
- Mucosal DNA and RNA virome alterations and their interactions with human RNA and microRNA transcriptomes in colorectal polyps. 2025 PMID 40964170 PMC12439157 own_data
Archive description
This study examine the relationship betweem mucosal virome and transcriptome in colorectal neoplasia and their adjacent normal tissues.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Colorectal neoplasia”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46254550 | collection_date | 2017-09-05 | R1 | 0.90 | biosample.attribute:collection_date | 2017-09-05 |
| SAMN46254550 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia |
| SAMN46254550 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | N0007 |
| SAMN46254550 | health_condition_detail | N0007 | R1 | 0.70 | sample.name_rule:alias | N0007 |
| SAMN46254550 | latitude | -33.8700 | R1 | 0.90 | biosample.attribute:lat_lon | 33.87 S 151.20 E |
| SAMN46254550 | location_site | Westmead Hospital | R3 | 0.70 | paper.fulltext.methods | recruited from Westmead Hospital |
| SAMN46254550 | longitude | 151.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 33.87 S 151.20 E |
| SAMN46254550 | subject_id | 0007 | R1 | 0.70 | sample.name_rule:alias | N0007 |
| SAMN46254590 | subject_id | 100003509 | R1 | 0.70 | biosample.attribute:TITLE | 100003509 |
Sequencing
94 runs over 94 samples · mean 9.06 Gbp per run (median 10.06 Gbp, total 851.45 Gbp; 94 runs with a base count) · layout PAIRED 94 · platform ILLUMINA 94 · models Illumina NovaSeq 6000 (94) · 87% of runs with a Sandpiper profile · first public 2025-10-31
Authors (10)
So SHS first · Jiang W · Li Y · Hold GL · Goodrick K · Min A · Bourke MJ · El-Omar EM · Jiang XT · Yim HCH last
Downloads
PRJNA1210680.csv.gz (3.6 KB) · parquet (74.6 KB) — all 94 samples, every field with route and confidence · PRJNA1210680_determinations.csv.gz (6.7 KB) — 712 evidence rows