Gut metagenomics in GH-secreting pituitary adenoma
19 gut metagenome samples from a case-control study comparing patients with GH-secreting pituitary adenoma and healthy controls, analyzed by shotgun metagenomic sequencing for species-level taxonomic and functional differences. machine-written summary
19 samples · 19 runs · CN · Adult · 2022 · 5.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 35 sample values (age, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 19 sample values (subject id) · PMC8754134 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 81 sample values (antibiotic exposure, bmi, country, health condition, health condition detail) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: sequence archive and Meta2DB disagree for 9 samples (e.g. 5844.0 vs 16801.5) — withheld; sex: sequence archive and Meta2DB disagree for 8 samples (e.g. male vs female) — withheld.
The sources disagree on 14 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 (17)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN21155464 | age | 5844.0 (sequence archive) | 16801.5 (Meta2DB) | withheld: neither value published |
| SAMN21155465 | age | 11305.8 (sequence archive) | 16801.5 (Meta2DB) | withheld: neither value published |
| SAMN21155466 | age | 11688.0 (sequence archive) | 14975.2 (Meta2DB) | withheld: neither value published |
| SAMN21155467 | age | 18993.0 (sequence archive) | 14244.8 (Meta2DB) | withheld: neither value published |
| SAMN21155468 | age | 20454.0 (sequence archive) | 9496.5 (Meta2DB) | withheld: neither value published |
| SAMN21155469 | age | 15704.0 (sequence archive) | 11322.8 (Meta2DB) | withheld: neither value published |
| SAMN21155471 | age | 16791.8 (sequence archive) | 9861.8 (Meta2DB) | withheld: neither value published |
| SAMN21155472 | age | 12418.5 (sequence archive) | 8035.5 (Meta2DB) | withheld: neither value published |
| SAMN21155481 | age | 19358.2 (sequence archive) | 14975.2 (Meta2DB) | withheld: neither value published |
| SAMN21155464 | sex | male (sequence archive) | female (Meta2DB) | withheld: neither value published |
| SAMN21155466 | sex | male (sequence archive) | female (Meta2DB) | withheld: neither value published |
| SAMN21155470 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
| SAMN21155471 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
| SAMN21155473 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
| SAMN21155474 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
| SAMN21155475 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
| SAMN21155479 | sex | female (sequence archive) | male (Meta2DB) | withheld: neither value published |
Genera, mean relative abundance over 18 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 | 19 | 100% | ||||
| country | 19 | 100% | 19 | |||
| health_condition | 19 | 100% | 7 | 12 | ||
| subject_id | 19 | 100% | 19 | |||
| antibiotic_exposure | 19 | 100% | 19 | |||
| bmi | 19 | 100% | 19 | |||
| health_condition_detail | 19 | 100% | 7 | 12 | ||
| sex | 11 | 58% | 11 | |||
| age_at_collection_days | 10 | 53% | 10 |
- Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma. 2022 PMID 35019688 PMC8754134 own_data
Archive description
The current study illustrated the metagenomic construction and characteristics of patients with growth hormone secreting pituitary adenoma.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “growth hormone secreting pituitary adenoma”
- body site sample.attr.tissue · “feces (n=19/19)”
- life stage sample.attr.age · “53 (n=18/19)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21155470 | age_at_collection_days | 13149.0 | R1 | 0.85 | sample.attr.age | 36 |
| SAMN21155464 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN21155464 | bmi | 32.05 | R2 | 0.70 | external.meta2db source | host_body_mass_index: 32.05 kilogram per meter squared |
| SAMN21155464 | country | CN | R2 | 0.70 | external.meta2db source | geo_loc_name: China:Shanghai |
| SAMN21155474 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | HC_metagenome_02 |
| SAMN21155464 | health_condition | other_cancer | R2 | 0.70 | external.meta2db source | growth hormone secreting pituitary adenoma |
| SAMN21155474 | health_condition_detail | healthy control | R1 | 0.70 | sample.name_rule:alias | HC_metagenome_02 |
| SAMN21155464 | health_condition_detail | growth hormone secreting pituitary adenoma | R2 | 0.70 | external.meta2db source | growth hormone secreting pituitary adenoma |
| SAMN21155465 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN21155464 | subject_id | SAMN21155464 | R3 | 0.70 | design.one_sample_per_subject:fulltext | stool samples of 9 patients and 10 healthy controls were randomly selected and further analyzed by metagenomics sequencing |
Sequencing
19 runs over 19 samples · mean 6.99 Gbp per run (median 5.77 Gbp, total 132.90 Gbp; 19 runs with a base count) · layout PAIRED 19 · platform ILLUMINA 19 · models Illumina HiSeq 1500 (19) · 95% of runs with a Sandpiper profile · first public 2022-01-02
Authors (24)
Lin B first · Wang M · Gao R · Ye Z · Yu Y · He W · Qiao N · Ma Z · Ji C · Shi C · Zhou X · Wang Y · Zeng F · Zhang L · Gong W · Cao Z · Zhou P · Melnikov V · Ye H · Li Y · Zhang Z · He M · Qin H · Zhang Y last
Downloads
PRJNA759070.csv.gz (1.6 KB) · parquet (71.1 KB) — all 19 samples, every field with route and confidence · PRJNA759070_determinations.csv.gz (2.9 KB) — 135 evidence rows