SFB metagenome in infant intestinal samples, Hangzhou, China
11 samples from infants in Hangzhou, China, examining segmented filamentous bacteria (SFB) sequences to compare differences between mouse and human. Design not reported. machine-written summary
11 samples · 11 runs · CN · Infant / toddler · 2017 · 3.87 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 22 sample values (country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 11 sample values (location locality) · PMC6034559 |
| ○ 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 |
longitudinal — not resolved
4 of 6 people sampled more than once (9 samples; median 2, up to 3 per person).
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 | 11 | 100% | ||||
| country | 11 | 100% | 11 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 11 | 100% | 11 | |||
| detailed_location | 11 | 100% | ||||
| location_locality | 11 | 100% | 11 |
- Genome sequence of segmented filamentous bacteria present in the human intestine. 2020 PMID 32887924 PMC7474095 cites_accession
- Presence of Segmented Filamentous Bacteria in Human Children and Its Potential Role in the Modulation of Human Gut Immunity. 2018 PMID 30008704 PMC6034559 own_data
Archive description
To find out the differences of SFB sequences between mouse and human
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “children intestinal bacteria about SFB”
- 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 · “children intestinal bacteria about”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR3147679 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Hangzhou |
| SRR3147679 | location_locality | Hangzhou | R3 | 0.70 | paper.body.text | 144 individuals in Hangzhou, China (80 males, 64 females; 2 months to 178 months-of-age) were enrolled in our SFB study |
| SRR3147679 | subject_id | 1 | R1 | 0.70 | sample.name_rule:library_name | A1-2 |
Sequencing
11 runs over 11 samples · mean 4.03 Gbp per run (median 3.87 Gbp, total 44.36 Gbp; 11 runs with a base count) · layout PAIRED 11 · platform ILLUMINA 11 · models Illumina HiSeq 2000 (11) · 91% of runs with a Sandpiper profile · first public 2017-02-05
Authors (0)
No author record.
Downloads
PRJNA299342.csv.gz (1.0 KB) · parquet (68.8 KB) — all 11 samples, every field with route and confidence · PRJNA299342_determinations.csv.gz (828 B) — 33 evidence rows