Gut mycobiota in children with thalassemia after HSCT, Turkey
62 stool samples from children with thalassemia undergoing allogeneic hematopoietic stem cell transplantation, plus donors and caregivers, in Turkey; longitudinal shotgun metagenomic study of gut mycobiota composition around the transplant. machine-written summary
62 samples · 62 runs · TR · Child · 2022 · 1.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 406 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 124 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 | 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 · population other_disease · Allogeneic hematopoietic stem cell transplantation, sampled before/after
“children with thalassemia undergoing aHSCT were enrolled” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
10 of 10 people sampled more than once (48 samples; median 5, up to 5 per person). Schedule stated by the source: “before transplantation regimen, within 72h before transplant day, +15, +30 days, and three months after transplantation” (time origin: transplant); stated follow-up 3 mo.
Genera, mean relative abundance over 43 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 | 62 | 100% | ||||
| country | 62 | 100% | 62 | |||
| health_condition | 62 | 100% | 62 | |||
| subject_id | 48 | 77% | 48 | |||
| collection_date | 62 | 100% | 62 | |||
| detailed_location | 62 | 100% | ||||
| health_condition_detail | 62 | 100% | 62 | |||
| latitude | 62 | 100% | 62 | |||
| location_region | 62 | 100% | 62 | |||
| longitude | 62 | 100% | 62 | |||
| timepoint_label | 48 | 77% | 48 |
- Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation. 2022 PMID 34699120 own_data
Archive description
Ten children with thalassemia undergoing aHSCT were enrolled. The stool samples were collected before the transplantation regimen, within 72 hours before the transplant day, +15, +30 days, and three months after transplantation. Stool samples were also collected from the donor and the patient’s caregivers.Gut mycobiota composition was evaluated with metagenomic analysis, using a shotgun sequencing with the Illumina NextSeq with 150 bp x2 chemistry.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “Intestinal mycobiota composition of”
- body site study.description · “were enrolled. The stool samples were collected”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “mycobiota composition of children with thalassemia undergoing”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8948078 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA8948078 | country | TR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Turkey |
| SAMEA8948078 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | children with thalassemia undergoing aHSCT |
| SAMEA8948078 | health_condition_detail | Children with thalassemia undergoing allogeneic hematopoietic stem cell transplantation | R4 | 0.50 | study.description | children with thalassemia undergoing aHSCT |
| SAMEA8948078 | latitude | 39.9272 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.9272 32.8644 |
| SAMEA8948078 | location_region | Ankara | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.9272 32.8644 |
| SAMEA8948078 | longitude | 32.8644 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.9272 32.8644 |
| SAMEA8948078 | subject_id | patient_1 | R1 | 0.70 | sample.name_rule:sample_alias | 57_C11 |
| SAMEA8948078 | timepoint_label | T1 | R1 | 0.60 | sample.name_rule:sample_alias | 57_C11 |
Sequencing
62 runs over 62 samples · mean 1.22 Gbp per run (median 1.24 Gbp, total 75.81 Gbp; 62 runs with a base count) · layout PAIRED 62 · platform ILLUMINA 62 · models NextSeq 500 (62) · 69% of runs with a Sandpiper profile · first public 2022-02-10
Authors (0)
No author record.
Downloads
PRJEB46003.csv.gz (2.5 KB) · parquet (72.5 KB) — all 62 samples, every field with route and confidence · PRJEB46003_determinations.csv.gz (4.7 KB) — 530 evidence rows