Gut metagenomics before/after allo-HSCT in one AML patient, Germany
Two stool shotgun metagenomes from a single patient with acute myeloid leukaemia sampled before and after allogeneic stem-cell transplantation, Germany. machine-written summary
2 samples · 2 runs · DE · Age unknown · 2017 · 5.98 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 22 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · Allogeneic hematopoietic stem cell transplantation for AML, sampled before/after
“samples collected from a patient before and after treatment” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
1 of 1 people sampled more than once (2 samples; median 2, up to 2 per person) · follow-up median 4 mo (max 4 mo) · median interval between samples 4 mo (time from collection dates). Schedule stated by the source: “Collected 2014-02-28 (pre-transplant) and 2014-07-10 (post-transplant); exact relation to transplant date not given numerically” (time origin: transplant).
Each row is one person (1 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 2 | 100% | ||||
| country | 2 | 100% | 2 | |||
| health_condition | 2 | 100% | 2 | |||
| subject_id | 2 | 100% | 2 | |||
| age_at_collection_days | 2 | 100% | 2 | |||
| antibiotic_exposure | 2 | 100% | 2 | |||
| collection_date | 2 | 100% | 2 | |||
| health_condition_detail | 2 | 100% | 2 | |||
| latitude | 2 | 100% | 2 | |||
| longitude | 2 | 100% | 2 | |||
| sex | 2 | 100% | 2 | |||
| timepoint_label | 2 | 100% | 2 |
- Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation. 2017 PMID 28686852 own_data
Archive description
A detailed assessment of microbiota changes in relation to acute GvHD: metagenomic and metatranscriptomic shotgun sequencing data was performed on samples collected from a patient before and after treatment for acute myeloid leukemia.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.55. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (2)”
- host biosample_attributes.env_material · “stool (2)”
- body site runs.scientific_name · “human gut metagenome (2)”
- body site biosample_attributes.env_material · “stool (2)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04613413 | age_at_collection_days | 23011.0 | R1 | 0.85 | biosample.attribute:host_age | 63 years |
| SAMN04613413 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | antibiotics |
| SAMN04613413 | collection_date | 2014-02-28 | R1 | 0.85 | biosample.attribute:collection_date | 2014-02-28 |
| SAMN04613413 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany |
| SAMN04613413 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:host_disease | AML |
| SAMN04613413 | health_condition_detail | AML | R1 | 0.85 | biosample.attribute:host_disease | AML |
| SAMN04613413 | latitude | 49.3 | R1 | 0.85 | biosample.attribute:lat_lon | 49.3 N 7.3 E |
| SAMN04613413 | longitude | 7.3 | R1 | 0.85 | biosample.attribute:lat_lon | 49.3 N 7.3 E |
| SAMN04613413 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN04613414 | sex | female | R1 | 0.75 | biosample.attribute:host_sex | female |
| SAMN04613413 | subject_id | A07 | R1 | 0.70 | sample.name_rule:alias | A07-1 |
| SAMN04613413 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | A07-1 |
Sequencing
2 runs over 2 samples · mean 5.98 Gbp per run (median 5.98 Gbp, total 11.96 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models Illumina HiSeq 2500 (2) · 100% of runs with a Sandpiper profile · first public 2017-05-03
Authors (8)
Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last
Downloads
PRJNA317435.csv.gz (955 B) · parquet (70.4 KB) — all 2 samples, every field with route and confidence · PRJNA317435_determinations.csv.gz (875 B) — 22 evidence rows