Pediatric gut microbiome in type 1 diabetes and obesity
112 gut microbiome samples from pediatric (child and adolescent) subjects, examining links between type 1 diabetes, obesity, and autoimmune/inflammatory conditions; no country or design details specified. machine-written summary
112 samples · 112 runs · Child · 2022 · 0.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,006 sample values (age, antibiotic exposure, bmi, collection date, health condition, health condition detail, medication, medication detail) |
| – 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 |
sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 2 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA10987220 | sex | female (sequence archive) | subject OT1D023: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA10987221 | sex | male (sequence archive) | subject OT1D023: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA10987220 | subject id | OT1D023 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMEA10987221 | subject id | OT1D023 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 112 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 112 | 100% | 112 | |||
| subject_id | 110 | 98% | 110 | |||
| age_at_collection_days | 112 | 100% | 112 | |||
| antibiotic_exposure | 112 | 100% | 112 | |||
| bmi | 112 | 100% | 112 | |||
| collection_date | 112 | 100% | 112 | |||
| health_condition_detail | 112 | 100% | 112 | |||
| sex | 110 | 98% | 110 | |||
| medication | 65 | 58% | 65 | |||
| medication_detail | 49 | 44% | 49 |
Archive description
Type 1 diabetes (T1D) is the major type of childhood diabetes. In the last few decades, the prevalence of T1D has increased dramatically, particularly in children under 5 years of age. The rapid rise of T1D incidence coincidently follows the same trend as the outbreak of obesity, especially in developed countries. Indeed, epidemiological studies have revealed a strong association between obesity and the risk of T1D. Nearly 40% of pediatric T1D patients ages 2 to 18 years in the U.S. are obese or overweight. Excessive weight puts these children at higher risk for cardiovascular disease, which is the leading cause of death for T1D. However, we still lack the appropriate criteria to diagnose and treat these patients in order to prevent early morbidity and mortality. This is mainly due to the fact that we remain ignorant about how the natural history and disease pathogenesis of T1D are altered by overweight or obesity. To address this unmet need, we will employ a series of cutting-edge techniques to investigate the role of obesity in T1D pathogenesis in human subjects.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “Profiles in the Pediatric Population”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA10987109 | age_at_collection_days | 2593.3 | R1 | 0.90 | sample.attr.host_age | 7.1 |
| SAMEA10987109 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | no |
| SAMEA10987109 | bmi | 13.64 | R1 | 0.90 | sample.attr.host_body_mass_index | 13.64 |
| SAMEA10987109 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_timestamp | 2016 |
| SAMEA10987109 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:analysis_disease_stage_group | NH |
| SAMEA10987141 | health_condition | autoimmune_inflammatory | R1 | 0.85 | biosample_attr | yes |
| SAMEA10987109 | health_condition_detail | non-T1D + normal weight | R1 | 0.90 | sample.attr.analysis_disease_stage | non-T1D + normal weight |
| SAMEA10987109 | medication | corticosteroid | R1 | 0.90 | biosample.attribute:med_steroid_inhalation_any | yes |
| SAMEA10987141 | medication | antidiabetic_other | R1 | 0.85 | biosample.attribute:med_insulin_injection | med_insulin_injection: yes |
| SAMEA10987143 | medication | antidiabetic_other | R1 | 0.85 | biosample.attribute:med_insulin_injection;total_daily_insulin | med_insulin_injection: yes; total_daily_insulin: 0.87 |
| SAMEA10987184 | medication | metformin | R1 | 0.90 | biosample.attribute:med_metformin_oral | yes |
| SAMEA10987186 | medication | laxative | R1 | 0.90 | biosample.attribute:supp_laxative_oral_miralax | yes |
| SAMEA10987209 | medication | corticosteroid;immunosuppressant_or_biologic | R1 | 0.90 | biosample.attribute:med_steroid_topical_fluocinolone_oil | yes |
| SAMEA10987141 | medication_detail | med_insulin_injection: yes | R1 | 0.85 | biosample.attribute:med_insulin_injection | med_insulin_injection: yes |
| SAMEA10987143 | medication_detail | med_insulin_injection: yes; total_daily_insulin: 0.87 | R1 | 0.85 | biosample.attribute:med_insulin_injection;total_daily_insulin | med_insulin_injection: yes; total_daily_insulin: 0.87 |
| SAMEA10987109 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMEA10987109 | subject_id | NH001 | R1 | 0.85 | sample.attr.host_subject_id | NH001 |
Sequencing
112 runs over 112 samples · mean 0.35 Gbp per run (median 0.33 Gbp, total 38.95 Gbp; 112 runs with a base count) · layout PAIRED 112 · platform ILLUMINA 112 · models Illumina HiSeq 2500 (112) · 0% of runs with a Sandpiper profile · first public 2022-11-16
Authors (0)
No author record.
Downloads
PRJEB48814.csv.gz (5.1 KB) · parquet (77.1 KB) — all 112 samples, every field with route and confidence · PRJEB48814_determinations.csv.gz (9.6 KB) — 1,006 evidence rows