2bRAD-M method validation incl. 3 fecal samples, Shandong
3 fecal samples from healthy adults in Shandong province, China, used to test the 2bRAD-M species-resolved sequencing method for low-biomass/degraded microbiomes, alongside mock communities and FFPE samples. machine-written summary
3 samples · 3 runs · CN · Age unknown · 2021 · 133.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 15 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 9 sample values (health condition, health condition detail, subject id) · PMC8789378 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 3 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 | 3 | 100% | ||||
| country | 3 | 100% | 3 | |||
| health_condition | 3 | 100% | 3 | |||
| subject_id | 3 | 100% | 3 | |||
| collection_date | 3 | 100% | 3 | |||
| detailed_location | 3 | 100% | ||||
| health_condition_detail | 3 | 100% | 3 | |||
| latitude | 3 | 100% | 3 | |||
| location_region | 3 | 100% | 3 | |||
| longitude | 3 | 100% | 3 |
- Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M. 2022 PMID 35078506 PMC8789378 own_data
Archive description
Sequencing data used in the manuscript including (1) The sequencing data of 16S, WMS and 2bRAD-M for MOCK (MOCK CAS and ATCC MOCK MSA 1002) and FFPE (only 2bRAD-M sequencing data) (2) The sequencing data of 16S and 2bRAD-M for typical low biomass samples (underarm, home and car) and fecal samples (3) The ultra-deep WMS data of stool samples
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17204405 | collection_date | 2019-12-24 | R1 | 0.90 | biosample.attribute:collection_date | 2019-12-24 |
| SAMN17204405 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shandong province |
| SAMN17204405 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Three healthy adult individuals were enrolled as volunteers |
| SAMN17204405 | health_condition_detail | healthy adult individuals enrolled as volunteers | R3 | 0.70 | paper.fulltext.methods | Three healthy adult individuals were enrolled as volunteers |
| SAMN17204405 | latitude | 36.0700 | R1 | 0.90 | biosample.attribute:lat_lon | 36.07 N 120.25 E |
| SAMN17204405 | location_region | Shandong | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shandong province |
| SAMN17204405 | longitude | 120.2500 | R1 | 0.90 | biosample.attribute:lat_lon | 36.07 N 120.25 E |
| SAMN17204405 | subject_id | SAMN17204405 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Three healthy adult individuals were enrolled as volunteers, and fecal samples were collected |
Sequencing
3 runs over 3 samples · mean 131.27 Gbp per run (median 133.05 Gbp, total 393.80 Gbp; 3 runs with a base count) · layout PAIRED 3 · platform ILLUMINA 3 · models Illumina MiSeq (3) · 100% of runs with a Sandpiper profile · first public 2021-12-04
Authors (16)
Sun Z first · Huang S · Zhu P · Tzehau L · Zhao H · Lv J · Zhang R · Zhou L · Niu Q · Wang X · Zhang M · Jing G · Bao Z · Liu J · Wang S · Xu J last
Downloads
PRJNA689204.csv.gz (1010 B) · parquet (70.2 KB) — all 3 samples, every field with route and confidence · PRJNA689204_determinations.csv.gz (985 B) — 24 evidence rows