Mucosal virome in ulcerative colitis vs controls, China
Shotgun metagenomic sequencing of virus-like particle preparations from rectal mucosal biopsies of 167 subjects (91 ulcerative colitis, 76 healthy controls) across China and Hong Kong. machine-written summary
167 samples · 167 runs · HK, CN · Age unknown · 2019 · 9.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 334 sample values (collection date, country) |
| ✓ Abstract / description | 167 sample values (location region) |
| ✓ Full text | 167 sample values (subject id) · PMC6582748, PMC8201803 |
| ✓ Supplementary tables | 649 sample values (age, health condition, health condition detail, medication, medication detail, sex, smoking status) |
| – 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 | 59 | 35% | ||||
| country | 167 | 100% | 167 | |||
| health_condition | 167 | 100% | 167 | |||
| subject_id | 167 | 100% | 167 | |||
| collection_date | 167 | 100% | 167 | |||
| detailed_location | 167 | 100% | ||||
| health_condition_detail | 167 | 100% | 167 | |||
| location_region | 167 | 100% | 167 | |||
| age_at_collection_days | 63 | 38% | 63 | |||
| medication | 63 | 38% | 63 | |||
| medication_detail | 63 | 38% | 63 | |||
| sex | 63 | 38% | 63 | |||
| smoking_status | 63 | 38% | 63 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 cites_accession
- Gut mucosal virome alterations in ulcerative colitis. 2019 PMID 30842211 PMC6582748 own_data
Archive description
human gut mucosal virome metagenomics sequencing data
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.57. Assay shotgun_dna.
- host runs.isolation_source · “rectal biopsy”
- host papers[1].abstract · “mucosal virome and their functions in health and UC”
- body site runs.isolation_source · “rectal biopsy”
- body site papers[1].abstract · “mucosal virome and their functions in health and UC”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10408007 | age_at_collection_days | 10227.0 | R2 | 0.80 | paper.supp.gutjnl-2018-318131supp009.pdf[Supplementary Table 1][Age] | UC03 M 28 L3 ... Never |
| SAMN10408007 | collection_date | 2017-02-09 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017-02-09 |
| SAMN10408007 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong |
| SAMN10408007 | health_condition | ulcerative_colitis | R2 | 0.85 | paper.supp.gutjnl-2018-318131supp011.xlsx[Sheet1!Sample] | Sample: UC03; Libid: FCHL5HMCCXY_L5_wHAXPI074033-8 |
| SAMN10408007 | health_condition_detail | ulcerative colitis | R2 | 0.85 | paper.supp.gutjnl-2018-318131supp011.xlsx[Sheet1!Sample] | Sample: UC03; Libid: FCHL5HMCCXY_L5_wHAXPI074033-8 |
| SAMN10408007 | location_region | China | R4 | 0.50 | paper.abstract | three different geographical regions in China |
| SAMN10408007 | medication | other_medication | R2 | 0.80 | paper.supp.gutjnl-2018-318131supp009.pdf[Supplementary Table 1][Medical treatment] | UC03: Topical mesalazine Oral mesalazine |
| SAMN10408007 | medication_detail | Topical mesalazine Oral mesalazine | R2 | 0.80 | paper.supp.gutjnl-2018-318131supp009.pdf[Supplementary Table 1][Medical treatment] | UC03: Topical mesalazine Oral mesalazine |
| SAMN10408007 | sex | male | R2 | 0.80 | paper.supp.gutjnl-2018-318131supp009.pdf[Supplementary Table 1][Sex] | UC03 M 28 L3 ... Never |
| SAMN10408007 | smoking_status | never | R2 | 0.80 | paper.supp.gutjnl-2018-318131supp009.pdf[Supplementary Table 1][Smoking History] | UC03 M 28 L3 ... Never |
| SAMN10408007 | subject_id | SAMN10408007 | R3 | 0.70 | design.one_sample_per_subject:fulltext | mucosa of 167 subjects from three different geographical regions in China (UC=91; healthy controls=76) |
Sequencing
167 runs over 167 samples · mean 8.49 Gbp per run (median 9.39 Gbp, total 1,418.65 Gbp; 167 runs with a base count) · layout PAIRED 167 · platform ILLUMINA 167 · models HiSeq X Ten (167) · 92% of runs with a Sandpiper profile · first public 2019-03-09
Authors (18)
Zuo T first · Lu XJ · Zhang Y · Cheung CP · Lam S · Zhang F · Tang W · Ching JYL · Zhao R · Chan PKS · Sung JJY · Yu J · Chan FKL · Cao Q · Sheng JQ · Ng SC last · Tisza MJ first · Buck CB last
Downloads
PRJNA504921.csv.gz (6.0 KB) · parquet (79.5 KB) — all 167 samples, every field with route and confidence · PRJNA504921_determinations.csv.gz (13.8 KB) — 1,317 evidence rows