Sequencing technology comparison on elderly stool samples
Cross-sectional study comparing amplicon and shotgun sequencing methods (Illumina HiSeq, MiSeq, Ion PGM) using 6 stool samples from elderly individuals; no disease condition or intervention specified. machine-written summary
6 samples · 18 runs · Age unknown · 2016 · 5.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 6 sample values (subject id) · PMC4746063 |
| ○ 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 5 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 | 6 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 6 | 100% | 6 |
- Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis. 2016 PMID 26849217 PMC4746063 own_data
Archive description
The goals of this study were to compare sequencing technology results and investigate their 16S rRNA gene and Metagenomic sequencing ability.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Human Faecal Samples”
- body site study.title · “Human Faecal Samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04414075 | subject_id | SAMN04414075 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Stool samples were collected from six elderly individuals |
Sequencing
18 runs over 6 samples · mean 1.91 Gbp per run (median 0.73 Gbp, total 34.40 Gbp; 18 runs with a base count) · layout PAIRED 12, SINGLE 6 · platform ILLUMINA 12, ION_TORRENT 6 · models Illumina HiSeq 2000 (6), Illumina MiSeq (6), Ion Torrent PGM (6) · 39% of runs with a Sandpiper profile · first public 2016-02-16
Authors (7)
Clooney AG first · Fouhy F · Sleator RD · O' Driscoll A · Stanton C · Cotter PD · Claesson MJ last
Downloads
PRJNA308846.csv.gz (997 B) · parquet (68.5 KB) — all 6 samples, every field with route and confidence · PRJNA308846_determinations.csv.gz (447 B) — 6 evidence rows