Stool metagenomes in alloHSCT, Düsseldorf, longitudinal
113 stool samples from allogeneic hematopoietic stem cell transplant patients in Düsseldorf, Germany, collected at multiple timepoints during therapy in a longitudinal design, plus a 10-person control group and Zymo Gut Microbiome Standard samples. machine-written summary
113 samples · 113 runs · DE · Adult · 2023 · 2.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,218 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location locality, location region) |
| ✓ Abstract / description | 24 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10876974, PMC11836353, PMC12510455 |
| ✓ Supplementary tables | 104 sample values (age, sex) |
| – 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 |
longitudinal — not resolved
29 of 44 people sampled more than once (98 samples; median 3, up to 5 per person). Schedule stated by the source: “Stool collected longitudinally before transplantation (pre-Tx), during leukopenia, and during reconstitution for each patient, plus healthy controls” (time origin: transplant).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 113 | 100% | ||||
| country | 113 | 100% | 113 | |||
| health_condition | 113 | 100% | 101 | 12 | ||
| subject_id | 113 | 100% | 113 | |||
| collection_date | 113 | 100% | 113 | |||
| detailed_location | 113 | 100% | ||||
| health_condition_detail | 113 | 100% | 101 | 12 | ||
| latitude | 113 | 100% | 113 | |||
| location_locality | 113 | 100% | 113 | |||
| location_region | 113 | 100% | 113 | |||
| longitude | 113 | 100% | 113 | |||
| timepoint_label | 113 | 100% | 113 | |||
| intervention | 112 | 99% | 112 | |||
| sex | 101 | 89% | 101 | |||
| age_at_collection_days | 3 | 3% | 3 |
- Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. 2024 PMID 38374282 PMC10876974 own_data
- Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling. 2025 PMID 41066697 PMC12510455 own_data
- Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo. 2025 PMID 39966439 PMC11836353 unsure
Archive description
ONT WG sequencing of stool samples in alloHSCT patients taken at multiple timepoints throughout therapy as well as additional samples containing Zymo Gut Microbiome Std. and a control group of 10 individuals.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “ONT Sequencing of Stool Samples in alloHSCT”
- body site study.description · “WG sequencing of stool samples in alloHSCT”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32957174 | age_at_collection_days | 18628.0 | R2 | 0.75 | paper.supp.41598_2024_53506_MOESM23_ESM.xlsx[Tabelle1 (2)!Age at Tx] | 51 |
| SAMN32957172 | collection_date | 2018-06/2019-12 | R1 | 0.90 | biosample.attribute:collection_date | 2018-06/2019-12 |
| SAMN32957172 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany:Duesseldorf |
| SAMN32957172 | health_condition | transplant_or_immunocompromised | R1 | 0.85 | biosample.attribute:timephase | Pre TX |
| SAMN32957273 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | alloHSCT patients |
| SAMN32957172 | health_condition_detail | Pre TX | R1 | 0.85 | biosample.attribute:timephase | Pre TX |
| SAMN32957273 | health_condition_detail | allogeneic hematopoietic stem cell transplantation patients | R4 | 0.50 | study.description | alloHSCT patients |
| SAMN32957172 | intervention | other_intervention | R1 | 0.85 | biosample.attribute:timephase | Pre TX |
| SAMN32957172 | latitude | 51.2200 | R1 | 0.90 | biosample.attribute:lat_lon | 51.22 N 6.77 E |
| SAMN32957172 | location_locality | Düsseldorf | R1 | 0.75 | biosample.attribute:geo_loc_name | Germany:Duesseldorf |
| SAMN32957172 | location_region | North Rhine-Westphalia | R1 | 0.60 | biosample.attribute:lat_lon | 51.22 N 6.77 E |
| SAMN32957172 | longitude | 6.7700 | R1 | 0.90 | biosample.attribute:lat_lon | 51.22 N 6.77 E |
| SAMN32957172 | sex | male | R2 | 0.75 | paper.supp.41598_2024_53506_MOESM23_ESM.xlsx[Tabelle1 (2)!Sex] | 1 |
| SAMN32957172 | subject_id | 4 | R1 | 0.85 | biosample.attribute:PatID | 4 |
| SAMN32957284 | subject_id | Zymo_Power | R1 | 0.70 | sample.name_rule:alias | Zymo_Power_-100.fastq.gz |
| SAMN32957172 | timepoint_label | Pre TX | R1 | 0.85 | sample.attr.timephase | Pre TX |
| SAMN32957284 | timepoint_label | -100 | R1 | 0.70 | sample.name_rule:alias | Zymo_Power_-100.fastq.gz |
Sequencing
113 runs over 113 samples · mean 6.65 Gbp per run (median 2.16 Gbp, total 750.96 Gbp; 113 runs with a base count) · layout SINGLE 113 · platform OXFORD_NANOPORE 113 · models PromethION (113) · 0% of runs with a Sandpiper profile · first public 2023-12-19
Authors (24)
Spohr P first · Scharf S · Rommerskirchen A · Henrich B · Jäger P · Klau GW · Haas R · Dilthey A · Pfeffer K last · Chen X first · Yin X · Xu X · Zhang T last · Li Y first · Gao Y · Liu X · Mao Y · Wang M · Qin Y · Zhang C · Chen Q · Ning K · Wang Z · Han M last
Downloads
PRJNA929328.csv.gz (4.1 KB) · parquet (76.2 KB) — all 113 samples, every field with route and confidence · PRJNA929328_determinations.csv.gz (9.7 KB) — 1,346 evidence rows