Fecal preservation method test, 121 samples, China
Cross-sectional study of 121 fecal samples from healthy individuals in China, testing an N-octylpyridinium bromide-based reagent for room-temperature storage and transport while preserving bacterial composition for up to 14 days. machine-written summary
121 samples · 121 runs · CN · Age unknown · 2017 · 2.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 605 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 242 sample values (health condition, health condition detail) · PMC5828344 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 121 | 100% | 121 | |||
| health_condition | 121 | 100% | 121 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 121 | 100% | 121 | |||
| detailed_location | 121 | 100% | ||||
| health_condition_detail | 121 | 100% | 121 | |||
| latitude | 121 | 100% | 121 | |||
| location_region | 121 | 100% | 121 | |||
| longitude | 121 | 100% | 121 |
- A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses. 2018 PMID 29482661 PMC5828344 own_data
Archive description
Background: The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing. Results: In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method, and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days.Conclusions: We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “storage of fecal samples at room temperature”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104407249 | collection_date | 2015-10 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10 |
| SAMEA104407249 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA104407249 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Eight subjects provided fecal samples in a stool container |
| SAMEA104407249 | health_condition_detail | not stated as having any disease; method-validation subjects | R3 | 0.70 | paper.fulltext.methods | Eight subjects provided fecal samples in a stool container |
| SAMEA104407249 | latitude | 22.6200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.62 114.07 |
| SAMEA104407249 | location_region | Guangdong | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.62 114.07 |
| SAMEA104407249 | longitude | 114.0700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.62 114.07 |
Sequencing
121 runs over 121 samples · mean 1.90 Gbp per run (median 2.02 Gbp, total 229.91 Gbp; 121 runs with a base count) · layout SINGLE 121 · platform ILLUMINA 97, BGISEQ 24 · models Illumina HiSeq 4000 (97), BGISEQ-500 (24) · 0% of runs with a Sandpiper profile · first public 2017-12-12
Authors (27)
Han M first · Hao L · Lin Y · Li F · Wang J · Yang H · Xiao L · Kristiansen K · Jia H · Li J last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB23662.csv.gz (3.8 KB) · parquet (74.6 KB) — all 121 samples, every field with route and confidence · PRJEB23662_determinations.csv.gz (5.1 KB) — 847 evidence rows