Infant cholestasis gut microbiota case-control study in Taiwan
Gut microbiota data from 10 samples collected from infants with various types of cholestasis in Taiwan, using a case-control design. machine-written summary
10 samples · 10 runs · TW · Infant / toddler · 2024 · 8.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 20 sample values (antibiotic exposure, location site) · PMC11246047 |
| ○ 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 |
Genera, mean relative abundance over 10 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 | 10 | 100% | 10 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 10 | 100% | 10 | |||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| location_site | 10 | 100% | 10 |
- Gut <i>Bifidobacterium longum</i> is associated with better native liver survival in patients with biliary atresia. PMID 39006502 PMC11246047 curated
Archive description
Microbiota sequence data of various types of infant cholestasis in Taiwan
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Microbiota of infant cholestasis in Taiwan”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39109984 | antibiotic_exposure | yes | R3 | 0.50 | paper.fulltext.methods | all patients with BA received antibiotics |
| SAMN39109984 | collection_date | 2016-03-07 | R1 | 0.85 | biosample.attribute:collection_date | 2016-03-07 |
| SAMN39109984 | country | TW | R1 | 0.90 | biosample_attr | Taiwan |
| SAMN39109984 | location_site | National Taiwan University Children's Hospital | R3 | 0.70 | paper.fulltext.methods | study was conducted at the National Taiwan University Children's Hospital |
Sequencing
10 runs over 10 samples · mean 7.84 Gbp per run (median 8.42 Gbp, total 78.37 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina NovaSeq 6000 (10) · 100% of runs with a Sandpiper profile · first public 2024-08-02
Downloads
PRJNA1056831.csv.gz (1.2 KB) · parquet (69.8 KB) — all 10 samples, every field with route and confidence · PRJNA1056831_determinations.csv.gz (954 B) — 40 evidence rows