PI-ME/CFS case-control study, Bethesda, USA
32 samples from adults in Bethesda, USA, comparing post-infectious myalgic encephalomyelitis/chronic fatigue syndrome cases (15) to healthy controls (17) in a case/control design. machine-written summary
32 samples · 32 runs · US · Adult · 2023 · 5.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 352 sample values (age, collection date, country, health condition, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 32 sample values (health condition detail) |
| ✓ Full text | 32 sample values (location site) · PMC10881493 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 30 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 | 32 | 100% | ||||
| country | 32 | 100% | 32 | |||
| health_condition | 32 | 100% | 32 | |||
| subject_id | 32 | 100% | 32 | |||
| age_at_collection_days | 32 | 100% | 32 | |||
| collection_date | 32 | 100% | 32 | |||
| detailed_location | 32 | 100% | ||||
| health_condition_detail | 32 | 100% | 32 | |||
| latitude | 32 | 100% | 32 | |||
| location_locality | 32 | 100% | 32 | |||
| location_region | 32 | 100% | 32 | |||
| location_site | 32 | 100% | 32 | |||
| longitude | 32 | 100% | 32 | |||
| sex | 32 | 100% | 32 | |||
| timepoint_label | 32 | 100% | 32 |
- Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome. 2024 PMID 38383456 PMC10881493 own_data
Archive description
Case/control research study of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.age · “54 (n=30/32)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38688091 | age_at_collection_days | 20454.0 | R1 | 0.70 | sample.attr.age | 56 |
| SAMN38688091 | collection_date | 2018-11-06 | R1 | 0.90 | biosample.attribute:collection_date | 2018-11-06 |
| SAMN38688091 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Bethesda |
| SAMN38688091 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | HV |
| SAMN38688091 | health_condition_detail | mixed_case_control: PI-ME/CFS patients vs matched controls | R4 | 0.50 | study.description | Case/control research study of post-infectious myalgic |
| SAMN38688091 | latitude | 39.0021 | R1 | 0.90 | biosample.attribute:lat_lon | 39.0021 N 77.1045 W |
| SAMN38688091 | location_locality | Bethesda | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Bethesda |
| SAMN38688091 | location_region | Maryland | R1 | 0.60 | biosample.attribute:lat_lon | 39.0021 N 77.1045 W |
| SAMN38688091 | location_site | NIH Clinical Center | R3 | 0.70 | paper.fulltext.methods | admitted to the NIH Clinical Center for a phenotyping visit |
| SAMN38688091 | longitude | -77.1045 | R1 | 0.90 | biosample.attribute:lat_lon | 39.0021 N 77.1045 W |
| SAMN38688091 | sex | female | R1 | 0.90 | sample.attr.gender | female |
| SAMN38688091 | subject_id | SID_16 | R1 | 0.85 | sample.attr.subject_id | SID_16 |
| SAMN38688091 | timepoint_label | v1 | R1 | 0.85 | sample.attr.visit | v1 |
Sequencing
32 runs over 32 samples · mean 5.88 Gbp per run (median 5.97 Gbp, total 188.08 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina NovaSeq 6000 (32) · 94% of runs with a Sandpiper profile · first public 2023-12-10
Authors (71)
Walitt B first · Singh K · LaMunion SR · Hallett M · Jacobson S · Chen K · Enose-Akahata Y · Apps R · Barb JJ · Bedard P · Brychta RJ · Buckley AW · Burbelo PD · Calco B · Cathay B · Chen L · Chigurupati S · Chen J · Cheung F · Chin LMK · Coleman BW · Courville AB · Deming MS · Drinkard B · Feng LR · Ferrucci L · Gabel SA · Gavin A · Goldstein DS · Hassanzadeh S · Horan SC · Horovitz SG · Johnson KR · Govan AJ · Knutson KM · Kreskow JD · Levin M · Lyons JJ · Madian N · Malik N · Mammen AL · McCulloch JA · McGurrin PM · Milner JD · Moaddel R · Mueller GA · Mukherjee A · Muñoz-Braceras S · Norato G · Pak K · Pinal-Fernandez I · Popa T · Reoma LB · Sack MN · Safavi F · Saligan LN · Sellers BA · Sinclair S · Smith B · Snow J · Solin S · Stussman BJ · Trinchieri G · Turner SA · Vetter CS · Vial F · Vizioli C · Williams A · Yang SB · Center for Human Immunology, Autoimmunity, and Inflammation (CHI) Consortium · Nath A last
Downloads
PRJNA954397.csv.gz (2.3 KB) · parquet (73.0 KB) — all 32 samples, every field with route and confidence · PRJNA954397_determinations.csv.gz (4.2 KB) — 416 evidence rows