Viral metagenome of fecal samples from children, Jiangsu
Cross-sectional study of 9 fecal virome samples pooled from neonates and healthy children in Zhenjiang, Jiangsu, China, collected Sep.–Dec. 2018 and analyzed by viral metagenomic sequencing. machine-written summary
9 samples · 9 runs · CN · Infant / toddler · 2022 · 0.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 19 sample values (collection date, country, health condition, health condition detail, location locality, location region, subject id) |
| ✓ Abstract / description | 9 sample values (location site) |
| ✓ Full text | 24 sample values (collection date, location locality, location region) · PMC10045071 |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 3 | 33% | 3 | |||
| subject_id | 1 | 11% | 1 | |||
| collection_date | 9 | 100% | 1 | 8 | ||
| detailed_location | 9 | 100% | ||||
| location_locality | 9 | 100% | 1 | 8 | ||
| location_region | 9 | 100% | 1 | 8 | ||
| location_site | 9 | 100% | 9 | |||
| health_condition_detail | 3 | 33% | 3 |
- Comparison of gut viral communities in children under 5 years old and newborns. PMID 36973710 PMC10045071 curated
Archive description
For viral metagenomic analysis, 90 Fecal specimens were collected from 45 neonates who were born in the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital from Sep. to Dec. 2018. Each specimen was added 200 to 500 ul DPBS. And then each specimen was shaken for 5 minutes and repeated it three times. The supernatants were collected after centrifugation. Then the 90 supernatants were randomly pooled into 10 specimen pools, each including 9 specimens. Supernatants were filtered through a 0.45-mm filter (Millipore) to remove eukaryotic- and bacterial cell-sized particles, and 200 uL of supernatant from each pool was then subjected to a mixture of nuclease enzymes to reduce the concentration of free (non-viral encapsidated) nucleic acids. Remaining total nucleic acid was then isolated using QIAamp MinElute Virus Spin Kit according to manufacturer's protocol. Ten libraries were then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced using the Illumina sequencing platform with 250 bases paired ends with dual barcoding for each pool.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “metagenomic analysis, 90 Fecal specimens were collected”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “collected from 45 neonates who were born”
- life stage study.description · “and 45 healthy children who were examined”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30410260 | collection_date | 2018-09/2018-12 | R1 | 0.90 | biosample.attribute:collection_date | 2018-09/2018-12 |
| SRR21195639 | collection_date | 2018-09/2018-12 | R3 | 0.70 | paper.fulltext.methods | examined at the same hospital from Sep. to Dec. 2018 |
| SAMN30410260 | country | CN | R1 | 0.90 | biosample_attr | China:Zhenjiang,Jiangsu |
| SRR21195639 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Zhenjiang,Jiangsu |
| SRR21195639 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:library_names | children02 |
| SRR21195639 | health_condition_detail | children | R1 | 0.70 | sample.name_rule:library_names | children02 |
| SAMN30410260 | location_locality | Zhenjiang | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Zhenjiang,Jiangsu |
| SRR21195639 | location_locality | Zhenjiang City | R3 | 0.70 | paper.fulltext.methods | Affiliated Hospital of Jiangsu University (Zhenjiang City, Jiangsu Province, China) |
| SAMN30410260 | location_region | Jiangsu | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Zhenjiang,Jiangsu |
| SRR21195639 | location_region | Jiangsu Province | R3 | 0.70 | paper.fulltext.methods | Affiliated Hospital of Jiangsu University (Zhenjiang City, Jiangsu Province, China) |
| SAMN30410260 | location_site | Affiliated Hospital of Jiangsu University | R4 | 0.45 | ena.study_description | born in the Affiliated Hospital of Jiangsu University |
| SAMN30410260 | subject_id | Newborns and children under 5 years of age | R1 | 0.50 | biosample_attr | Newborns and children under 5 years of age |
Sequencing
9 runs over 9 samples · mean 0.16 Gbp per run (median 0.13 Gbp, total 1.45 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina HiSeq 2500 (9) · 0% of runs with a Sandpiper profile · first public 2022-08-26 – 2022-08-28
Downloads
PRJNA869587.csv.gz (1.2 KB) · parquet (70.9 KB) — all 9 samples, every field with route and confidence · PRJNA869587_determinations.csv.gz (1.2 KB) — 52 evidence rows