Gut microbiome in Parkinson's disease, Vancouver case-control
Shotgun metagenomic sequencing (Illumina NovaSeq, 2x150 bp) of 290 samples from a Vancouver, Canada cohort, comparing gut microbiomes of people with and without Parkinson's disease in a case-control design. machine-written summary
290 samples · 290 runs · CA · Age unknown · 2024 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 580 sample values (collection date, country) |
| ✓ Abstract / description | 580 sample values (health condition detail, location locality) |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 290 | 100% | 290 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 290 | 100% | 290 | |||
| detailed_location | 290 | 100% | ||||
| health_condition_detail | 290 | 100% | 290 | |||
| location_locality | 290 | 100% | 290 |
- Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease. 2024 PMID 39192744 own_data
Archive description
This project contains all raw reads for the Metcalfe-Roach et. al (2024) papers describing the gut microbiome of people with and without Parkinson's disease in a Vancouver cohort. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform (2x150 bp), generating ~3.5 million reads per sample.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “gut microbiome of people with”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115471927 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA115471927 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA115471927 | health_condition_detail | mixed_case_control: Parkinson's disease patients vs healthy controls | R4 | 0.50 | study.description | people with and without Parkinson's disease |
| SAMEA115471927 | location_locality | Vancouver | R4 | 0.45 | ena.study_description | a Vancouver cohort |
Sequencing
290 runs over 290 samples · mean 0.47 Gbp per run (median 0.47 Gbp, total 135.61 Gbp; 290 runs with a base count) · layout PAIRED 290 · platform ILLUMINA 290 · models Illumina NovaSeq 6000 (290) · 0% of runs with a Sandpiper profile · first public 2024-04-23 – 2024-07-30
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB74553.csv.gz (7.9 KB) · parquet (81.3 KB) — all 290 samples, every field with route and confidence · PRJEB74553_determinations.csv.gz (7.6 KB) — 1,160 evidence rows