Gut metagenome in intraparenchymal hemorrhage, case-control
19 fecal shotgun metagenome samples from adult/elderly cerebral intraparenchymal hemorrhage patients and healthy controls, case-control design, examining gut bacterial composition and functional changes after brain injury. machine-written summary
19 samples · 20 runs · CN · Age unknown · 2022 · 13.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 57 sample values (age, health condition, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 38 sample values (location region, location site) · PMC8966894 |
| ✓ Supplementary tables | 26 sample values (subject id, timepoint) |
| ✓ External resources | 47 sample values (antibiotic exposure, country, health condition detail) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 17 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 | 19 | 100% | ||||
| country | 19 | 100% | 19 | |||
| health_condition | 19 | 100% | 19 | |||
| subject_id | 18 | 95% | 18 | |||
| age_at_collection_days | 19 | 100% | 19 | |||
| antibiotic_exposure | 19 | 100% | 19 | |||
| detailed_location | 19 | 100% | ||||
| location_region | 19 | 100% | 19 | |||
| location_site | 19 | 100% | 19 | |||
| sex | 19 | 100% | 19 | |||
| health_condition_detail | 9 | 47% | 9 | |||
| timepoint_label | 8 | 42% | 8 |
- Cerebral Intraparenchymal Hemorrhage Changes Patients' Gut Bacteria Composition and Function. 2022 PMID 35372117 PMC8966894 own_data
Archive description
This data was generated by shotgun sequencing for fecal samples from 10 patients after cerebral intraparenchymal hemorrhage and 10 feature-corresponding healthy controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host study.description · “fecal samples from 10 patients”
- body site study.description · “fecal samples from 10 patients”
- life stage sample.attr.age · “65 (n=11/19)”
- life stage sample.attr.age · “70 (n=8/19)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25943258 | age_at_collection_days | 24471.8 | R1 | 0.70 | sample.attr.age | 67 |
| SAMN25943258 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN25943258 | country | CN | R2 | 0.70 | external.meta2db source | geo_loc_name: China |
| SAMN25943258 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:library_name | patient1 |
| SAMN25943258 | health_condition_detail | cerebral intraparenchymal hemorrhage | R2 | 0.70 | external.meta2db source | cerebral intraparenchymal hemorrhage |
| SAMN25943258 | location_region | Hunan | R3 | 0.70 | paper.fulltext.methods | First Affiliated Hospital of Jishou University, Hunan, China |
| SAMN25943258 | location_site | First Affiliated Hospital of Jishou University | R3 | 0.70 | paper.fulltext.methods | First Affiliated Hospital of Jishou University, Hunan, China |
| SAMN25943258 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN25943258 | subject_id | patient1 | R2 | 0.85 | paper.supp.Table_1.xls[Tab S1 metadata!Samples] | patient1 |
| SAMN25943258 | timepoint_label | 2 days | R2 | 0.85 | paper.supp.Table_1.xls[Tab S1 metadata!Patients' Sample-Collecting Time After Cerebral Intraparenchymal Hemorrhage] | 2 days |
Sequencing
20 runs over 19 samples · mean 13.06 Gbp per run (median 13.08 Gbp, total 261.21 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina HiSeq 2500 (20) · 85% of runs with a Sandpiper profile · first public 2022-03-18
Downloads
PRJNA806955.csv.gz (1.7 KB) · parquet (71.7 KB) — all 19 samples, every field with route and confidence · PRJNA806955_determinations.csv.gz (2.8 KB) — 168 evidence rows