Gut microbiota in cystic fibrosis patients, cross-sectional
Cross-sectional metagenomic study of 495 gut microbiome samples from cystic fibrosis patients; location not specified. machine-written summary
496 samples · 496 runs · GB · Age unknown · 2023 · 40.2 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 743 sample values (subject id, timepoint) |
| ✓ Abstract / description | 2 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 1,485 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Each patient sampled at baseline (BL) and a later follow-up (FUP); exact interval not stated.”.
Genera, mean relative abundance over 219 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 | 495 | 100% | 495 | |||
| health_condition | 496 | 100% | 495 | 1 | ||
| subject_id | 496 | 100% | 496 | |||
| health_condition_detail | 496 | 100% | 495 | 1 | ||
| timepoint_label | 247 | 50% | 247 |
Archive description
Metagenomic analysis of gut microbiota in cystic fibrosis patients This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.description · “gut microbiota in cystic fibrosis patients”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110017300 | country | GB | R2 | 0.75 | external.gmrepo source | country: United Kingdom |
| SAMEA110017300 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMEA110130649 | health_condition | other_disease | R4 | 0.50 | study.description | cystic fibrosis patients |
| SAMEA110017300 | health_condition_detail | Cystic Fibrosis | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMEA110130649 | health_condition_detail | Study focuses on gut dysbiosis in cystic fibrosis | R4 | 0.50 | study.description | cystic fibrosis patients |
| SAMEA110017300 | subject_id | Igloo-CF10989556 | R1 | 0.85 | sample.attr.subject_id | Igloo-CF10989556 |
| SAMEA110130649 | subject_id | LS094 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: LS094_FUP_19212 |
| SAMEA110130453 | timepoint_label | BL | R1 | 0.70 | sample.name_rule:title | LS085_BL_19037 |
| SAMEA110130649 | timepoint_label | FUP | R1 | 0.70 | sample.name_rule:TITLE | TITLE: LS094_FUP_19212 |
Sequencing
496 runs over 496 samples · mean 3.59 Gbp per run (median 40.2 Mbp, total 1,781.24 Gbp; 496 runs with a base count) · layout PAIRED 496 · platform ILLUMINA 496 · models Illumina MiSeq (248), Illumina NovaSeq 6000 (248) · 44% of runs with a Sandpiper profile · first public 2023-06-16 – 2023-07-04
Authors (0)
No author record.
Downloads
PRJEB47458.csv.gz (12.2 KB) · parquet (89.2 KB) — all 496 samples, every field with route and confidence · PRJEB47458_determinations.csv.gz (20.6 KB) — 2,230 evidence rows