Faecal microbiota preservation method comparison study
60 faecal samples comparing nucleic acid fixation/stabilisation protocols (including RNAssist) against fresh-extracted control DNA to assess preservation of microbiota composition; intervention design. machine-written summary
60 samples · 60 runs · Age unknown · 2019 · 0.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 60 sample values (subject id) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 60 | 100% | 60 |
Archive description
The study aim is to examine the effect of various nucleic acid fixation/stabilisation protocols on the microbiota composition of faecal samples. Comparison of the fixed/stabilised samples with control DNA extracted from the fresh sample prior to fixation will give a picture of how well all the components of the microbiota are preserved. The ultimate goal, should one of the nucleic acid preservation methods return data sufficiently similar to freshly processed control, is to simplify sample collection and processing in the clinic and in the field. Extraction of DNA from a fresh sample remains the gold standard for faecal microbiota studies. Where preservation cannot be avoided samples are often frozen or suspended in alcohol, unfortunately this commonly results in the under-representation of phyla such as the Bacteroidetes in extracted DNA. Cells lyse during preservation their genomic DNA lost during sample processing required for the remainder of the faecal sample. Should RNAssist prove capable of preserving the entire composition of the faecal microbiota and return a breakdown comparable to that of the fresh control, this would be a step towards significantly easier sample collection and processing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.description · “simplify sample collection and processing in the clinic”
- body site study.description · “microbiota composition of faecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104694679 | subject_id | RNAss_MB7351537 | R1 | 0.85 | sample.attr.subject_id | RNAss_MB7351537 |
Sequencing
60 runs over 60 samples · mean 0.11 Gbp per run (median 0.11 Gbp, total 6.43 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models Illumina MiSeq (60) · 0% of runs with a Sandpiper profile · first public 2019-04-02
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJEB25227.csv.gz (2.1 KB) · parquet (70.5 KB) — all 60 samples, every field with route and confidence · PRJEB25227_determinations.csv.gz (881 B) — 60 evidence rows