Gut 16S metagenome, ulcerative colitis, 5-ASA therapy
118 gut bacterial metagenome samples from ulcerative colitis patients in Beijing, China, studying the effect of 5-aminosalicylic acid drug therapy on gut microbiota in a cross-sectional design. machine-written summary
119 samples · 119 runs · CN · Age unknown · 2022 · 59.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 432 sample values (country, intervention, location locality, subject id, timepoint) |
| ✓ Abstract / description | 238 sample values (health condition, health condition detail) |
| ✓ Full text | 238 sample values (collection date, location site) · PMC6008376 |
| ○ 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
Non-antibiotic pharmaceutical given as the study intervention (metformin design non_randomized_controlled · population ulcerative_colitis · 5-aminosalicylic acid (5-ASA) treatment vs untreated UC patients
“37 5-ASA-treated, were recruited” — abstract:29951050 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
38 of 51 people sampled more than once (104 samples; median 2, up to 6 per person). Schedule stated by the source: “mucosal samples before and after 5-ASA treatment (~6 months in 6 patients, ~12 months in 4 patients)” (time origin: intervention_start).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 119 | 100% | 119 | |||
| health_condition | 119 | 100% | 119 | |||
| subject_id | 117 | 98% | 117 | |||
| collection_date | 119 | 100% | 119 | |||
| detailed_location | 119 | 100% | ||||
| health_condition_detail | 119 | 100% | 119 | |||
| location_site | 119 | 100% | 119 | |||
| location_locality | 118 | 99% | 118 | |||
| intervention | 39 | 33% | 39 | |||
| timepoint_label | 39 | 33% | 39 |
- 5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis. 2018 PMID 29951050 PMC6008376 own_data
Archive description
HUMAN GUT BACTERIA
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 study.description · “HUMAN GUT BACTERIA”
- body site study.title · “GUT BACTERIAL METAGENOME”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08730699 | collection_date | 2015-01/2017-01 | R3 | 0.70 | paper.fulltext.methods | enrolled from Peking University People’s Hospital from January 2015 to January 2017 |
| SAMN08730699 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Beijing |
| SAMN08730699 | health_condition | ulcerative_colitis | R4 | 0.50 | paper.abstract | UC patients |
| SAMN08730699 | health_condition_detail | Ulcerative colitis | R4 | 0.50 | paper.abstract | UC patients |
| SAMN08730778 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:alias | K92-1N |
| SAMN08730699 | location_locality | Beijing | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Beijing |
| SAMN08730699 | location_site | Peking University People's Hospital | R3 | 0.70 | paper.fulltext.methods | enrolled from Peking University People’s Hospital |
| SAMN08730700 | subject_id | 9 | R1 | 0.70 | sample.name_rule:alias | 9N |
| SAMN08730778 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | K92-1N |
Sequencing
119 runs over 119 samples · mean 58.9 Mbp per run (median 59.6 Mbp, total 7.01 Gbp; 119 runs with a base count) · layout PAIRED 119 · platform ILLUMINA 119 · models Illumina HiSeq 2500 (119) · 0% of runs with a Sandpiper profile · first public 2022-03-21
Downloads
PRJNA439152.csv.gz (3.5 KB) · parquet (75.0 KB) — all 119 samples, every field with route and confidence · PRJNA439152_determinations.csv.gz (6.7 KB) — 908 evidence rows