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PRJNA943202 SRP426600

Pediatric IBD gut virome, Philadelphia, cross-sectional

Probing viral involvement in pediatric IBD

76 gut metagenome samples from children with IBD in Philadelphia, USA, collected in a cross-sectional design to probe viral involvement in pediatric IBD. machine-written summary

76 samples · 86 runs · US · Child · 2023 · 2.84 Gbp / sample

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Sources
✓Sequence archive 752–Abstract / description–Full text–Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive752 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
– Abstract / descriptionno abstract or project description
– Full textno open-access full text linked
– Supplementary tablesno supplementary tables available (or none open access)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
child76
Condition
ibd_unspecified76
Country
US76
Body site
primary76
Collected 2018–2020
2018: 33 samples2019: 41 samples2020: 2 samples20182020
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 3 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 49 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 23 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 2.84 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

28 of 40 people sampled more than once (56 samples; median 2, up to 2 per person) · follow-up median 7 mo (max 16 mo) · median interval between samples 7 mo (time from collection dates).

001001: day 0001: day 230004004: day 0004: day 228008008: day 0008: day 224010010: day 0010: day 252015015: day 0015: day 82017017: day 0017: day 189018018: day 0018: day 225024024: day 0024: day 204025025: day 0025: day 183028028: day 0028: day 232029029: day 0029: day 251034034: day 0034: day 45039039: day 0039: day 87042042: day 0042: day 97045045: day 0045: day 95046046: day 0046: day 210051051: day 0051: day 166056056: day 0056: day 97068068: day 0068: day 219077077: day 0077: day 356104104: day 0104: day 277105105: day 0105: day 297111111: day 0111: day 208135135: day 0135: day 46184184: day 0184: day 481212212: day 0212: day 339232232: day 0232: day 126247247: day 0247: day 360 d4 mo8 mo12 mo16 mo

Each row is one person (28 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 12.7%Blautia_A 11.4%Faecalibacterium 8.1%Bacteroides 7.1%Roseburia 4.0%Mediterraneibacter 3.2%Streptococcus 2.8%Ruminococcoides 2.7%Phocaeicola 2.5%Gemmiger 2.4%Collinsella 2.4%Anaerostipes 2.2%not assigned to a genus 6.0%other genera 32.6%

Genera, mean relative abundance over 65 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category76 100%
country76 100%76
health_condition76 100%76
subject_id68 89%68
collection_date76 100%76
detailed_location76 100%
health_condition_detail76 100%76
latitude76 100%76
location_locality76 100%76
location_region76 100%76
longitude76 100%76
timepoint_label76 100%76
Details
Archive description

A study carried out to characterize the microbiome of pediatric IBD patients.

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_unknown_no_evidence”
  • body site external_curation.infant_catalog · “body_site_call stool”
  • life stage study.title · “viral involvement in pediatric IBD”
  • life stage study.description · “the microbiome of pediatric IBD patients.”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN33713255collection_date2018-08-16R10.90biosample.attribute:collection_date2018-08-16
SAMN33713255countryUSR10.90sample.attr.geo_loc_nameUSA: Philadelphia
SAMN33713255health_conditionibd_unspecifiedR10.70sample.name_rule:aliasPediatric IBD 0
SAMN33713255health_condition_detailIBDR10.70sample.name_rule:aliasPediatric IBD 0
SAMN33713255latitude39.9500R10.90biosample.attribute:lat_lon39.95 N 75.16 W
SAMN33713255location_localityPhiladelphiaR10.85biosample.attribute:geo_loc_nameUSA: Philadelphia
SAMN33713255location_regionPennsylvaniaR10.60biosample.attribute:lat_lon39.95 N 75.16 W
SAMN33713255longitude-75.1600R10.90biosample.attribute:lat_lon39.95 N 75.16 W
SAMN33713255subject_id001R10.70sample.name_rule:library_nameBaseline001Swb
SAMN33713255timepoint_labelBaselineR10.70sample.name_rule:library_nameBaseline001Swb
Sequencing

86 runs over 76 samples · mean 2.72 Gbp per run (median 2.80 Gbp, total 233.99 Gbp; 86 runs with a base count) · layout PAIRED 86 · platform ILLUMINA 86 · models Illumina NovaSeq 6000 (86) · 85% of runs with a Sandpiper profile · first public 2023-03-11

Authors (0)

No author record.

Downloads

PRJNA943202.csv.gz (3.3 KB) · parquet (74.6 KB) — all 76 samples, every field with route and confidence · PRJNA943202_determinations.csv.gz (7.0 KB) — 752 evidence rows

Samples (76 · every field this project has values for · hover a cell for its source)
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