Gut Metagenome/Metatranscriptome Method Comparison, USA
65 human gut microbiome samples from the USA, comparing different storage and nucleic acid extraction methods for metagenomic and metatranscriptomic sequencing. machine-written summary
65 samples · 65 runs · US · Age unknown · 2022 · 0.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 378 sample values (collection date, country, latitude, location region, longitude, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 52 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 | 65 | 100% | 65 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 65 | 100% | 65 | |||
| detailed_location | 65 | 100% | ||||
| latitude | 65 | 100% | 65 | |||
| location_region | 65 | 100% | 65 | |||
| longitude | 65 | 100% | 65 | |||
| timepoint_label | 53 | 82% | 53 |
Archive description
Metagenomic and metatranscriptomic sequence reads of human gut microbiome under different sample storage and nucleic acid extraction conditions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.title · “Human Gut Metagenome”
- body site study.description · “human gut microbiome under different sample storage”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31389111 | collection_date | 2020-03-16 | R1 | 0.90 | biosample.attribute:collection_date | 2020-03-16 |
| SAMN31389111 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN31389111 | latitude | 26.1282 | R1 | 0.90 | biosample.attribute:lat_lon | 26.12815295 N 80.24827581 W |
| SAMN31389111 | location_region | Florida | R1 | 0.60 | biosample.attribute:lat_lon | 26.12815295 N 80.24827581 W |
| SAMN31389111 | longitude | -80.2483 | R1 | 0.90 | biosample.attribute:lat_lon | 26.12815295 N 80.24827581 W |
| SAMN31389111 | timepoint_label | technical replicate 1 | R1 | 0.85 | biosample.attribute:replicate | technical replicate 1 |
Sequencing
65 runs over 65 samples · mean 0.47 Gbp per run (median 0.51 Gbp, total 30.58 Gbp; 65 runs with a base count) · layout PAIRED 65 · platform ILLUMINA 65 · models NextSeq 550 (65) · 80% of runs with a Sandpiper profile · first public 2022-10-21
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA892575.csv.gz (2.5 KB) · parquet (72.3 KB) — all 65 samples, every field with route and confidence · PRJNA892575_determinations.csv.gz (2.8 KB) — 378 evidence rows