SSLR library prep method test, gut virome, Copenhagen
67 fecal virome and mock community samples from Copenhagen, Denmark, comparing a single-stranded ligation-based (SSLR) sequencing library preparation method against double-stranded and single-stranded alternatives. machine-written summary
67 samples · 67 runs · DK · Age unknown · 2025 · 0.68 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 402 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11515303 |
| ○ 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 23 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 | 0 | 0% | ||||
| country | 67 | 100% | 67 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 67 | 100% | 67 | |||
| detailed_location | 67 | 100% | ||||
| latitude | 67 | 100% | 67 | |||
| location_locality | 67 | 100% | 67 | |||
| location_region | 67 | 100% | 67 | |||
| longitude | 67 | 100% | 67 |
- A single-stranded based library preparation method for virome characterization. 2024 PMID 39449043 PMC11515303 own_data
Archive description
This dataset is used for single-stranded library preparation method testing of mock community and fecal virome by comparison of the other library preparation methods.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host study.description · “testing of mock community and fecal virome”
- body site study.description · “fecal virome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40702418 | collection_date | 2020-12 | R1 | 0.90 | biosample.attribute:collection_date | 2020-12 |
| SAMN40702418 | country | DK | R1 | 0.90 | sample.attr.geo_loc_name | Denmark: Copenhagen |
| SAMN40702418 | latitude | 55.6761 | R1 | 0.90 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
| SAMN40702418 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geo_loc_name | Denmark: Copenhagen |
| SAMN40702418 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
| SAMN40702418 | longitude | 12.5689 | R1 | 0.90 | biosample.attribute:lat_lon | 55.6761 N 12.5689 E |
Sequencing
67 runs over 67 samples · mean 0.67 Gbp per run (median 0.68 Gbp, total 45.07 Gbp; 67 runs with a base count) · layout PAIRED 67 · platform ILLUMINA 67 · models NextSeq 550 (39), Illumina NovaSeq 6000 (22), Illumina iSeq 100 (6) · 55% of runs with a Sandpiper profile · first public 2025-03-14 – 2025-03-23
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1094595.csv.gz (2.4 KB) · parquet (72.6 KB) — all 67 samples, every field with route and confidence · PRJNA1094595_determinations.csv.gz (2.7 KB) — 402 evidence rows