Human appendix microbiome across age and health groups
23 appendix microbiome samples spanning infant to elderly age categories, with most linked to gastrointestinal infection/diarrhoea; study characterizes gene, species, and functional content of the appendix microbiome. machine-written summary
23 samples · 23 runs · Age unknown · 2017 · 1.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 115 sample values (age, health condition, health condition detail, sex, subject id) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 13 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 | 23 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 23 | 100% | 23 | |||
| subject_id | 23 | 100% | 23 | |||
| age_at_collection_days | 23 | 100% | 23 | |||
| health_condition_detail | 23 | 100% | 23 | |||
| sex | 23 | 100% | 23 |
Archive description
Our study provides a new perspective of understanding appendix, a controversially functional human organ, by characterizing gene, species and functional contents of appendix microbiome.
How this project entered the registry
Classified as human other human site / gut / stool shotgun DNA metagenome of adult and child and elderly and adolescent by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.title · “Human Appendix Microbiome”
- body site study.title · “Human Appendix Microbiome”
- body site sample.attr.tissue · “appendix (n=23/23)”
- life stage sample.attr.age · “26 (n=11/23)”
- life stage sample.attr.age · “4 (n=5/23)”
- life stage sample.attr.age · “66 (n=4/23)”
- life stage sample.attr.age · “13 (n=3/23)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08162863 | age_at_collection_days | 1461.0 | R1 | 0.85 | sample.attr.age | 4 |
| SAMN08162863 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Acute simple appendicitis |
| SAMN08162863 | health_condition_detail | After appendectomy, the pathology of appendix showed acute appendicitis | R1 | 0.90 | sample.attr.health_state | After appendectomy, the pathology of appendix showed acute appendicitis |
| SAMN08162863 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN08162863 | subject_id | SAMN08162863 | R1 | 0.55 | design.one_sample_per_subject:archive | age 4; sex female; Acute simple appendicitis |
Sequencing
23 runs over 23 samples · mean 1.73 Gbp per run (median 1.23 Gbp, total 39.80 Gbp; 23 runs with a base count) · layout SINGLE 23 · platform ILLUMINA 23 · models Illumina HiSeq 4000 (23) · 57% of runs with a Sandpiper profile · first public 2017-12-14 – 2017-12-17
Authors (0)
No author record.
Downloads
PRJNA414153.csv.gz (1.7 KB) · parquet (70.6 KB) — all 23 samples, every field with route and confidence · PRJNA414153_determinations.csv.gz (2.0 KB) — 115 evidence rows