Gut virome in children with atopic dermatitis, Zhenjiang
Case-control study of 50 fecal samples from children in Zhenjiang, China, comparing gut virome composition between atopic dermatitis patients and healthy controls. machine-written summary
50 samples · 50 runs · CN · Child · 2020 · 0.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 100 sample values (health condition detail, location site) |
| ✓ Full text | 100 sample values (collection date, country) · PMC8899399 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 1 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 | 50 | 100% | ||||
| country | 50 | 100% | 50 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 50 | 100% | 50 | |||
| detailed_location | 50 | 100% | ||||
| health_condition_detail | 50 | 100% | 50 | |||
| location_site | 50 | 100% | 50 |
- Comparison of Gut Viral Communities in Atopic Dermatitis and Healthy Children. 2022 PMID 35265642 PMC8899399 own_data
Archive description
For viral metagenomic analysis, 50 feces samples were collected from 30 patients with atopic dermatitis and 20 health child who were admitted to the Department of Dermatology and Venerology of the Affiliated Hospital of Jiangsu University from Sep 2017 to Aug 2018. The mean age of study participants was 10.5 (8-13) years. The average courses were 3.263.14 month (1 week to 15 months). The 50 feces were randomly pooled into 50 specimen pools, each including 1 feces. The feces pools were individually homogenized with a mortar and pestle, resuspended in 1 mL DPBS, and then frozen and thawed rapidly three times on dry-ice. The supernatants were then collected after centrifugation (10 min, 15,000 g). 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[13,14]. Remaining total nucleic acid was then isolated using QIAamp MinElute Virus Spin Kit according to manufacturer's protocol. Eleven libraries were then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and sequenced using the MiSeq Illumina 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 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.description · “metagenomic analysis, 50 feces samples were collected”
- body site external_curation.infant_catalog · “body_site_call feces”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “and 20 health child who were admitted”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR12736145 | collection_date | 2017-09/2018-08 | R3 | 0.70 | paper.fulltext.methods | From September 2017 to August 2018 |
| SRR12736145 | country | CN | R3 | 0.70 | paper.fulltext.methods | Affiliated Hospital of Jiangsu University |
| SRR12736145 | health_condition_detail | mixed_case_control: Cohort includes both atopic dermatitis cases (30) and healthy controls (20) | R4 | 0.50 | study.description | 30 patients with atopic dermatitis and 20 health child |
| SRR12736145 | location_site | Affiliated Hospital of Jiangsu University | R4 | 0.45 | ena.study_description | Affiliated Hospital of Jiangsu University |
Sequencing
50 runs over 50 samples · mean 0.49 Gbp per run (median 0.42 Gbp, total 24.39 Gbp; 50 runs with a base count) · layout PAIRED 50 · platform ILLUMINA 50 · models Illumina HiSeq 2500 (50) · 16% of runs with a Sandpiper profile · first public 2020-09-30 – 2020-10-20
Authors (12)
Lu X first · Wang H · Zhang J · Jin K · Ma L · Wang Y · Yang S · Wang X · Shen Q · Zhou T · Xu H · Zhang W last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA666005.csv.gz (2.1 KB) · parquet (71.2 KB) — all 50 samples, every field with route and confidence · PRJNA666005_determinations.csv.gz (1.7 KB) — 200 evidence rows