Colonic mucosal transcriptome in UC patients receiving FMT
160 adult samples from ulcerative colitis patients in an FMT intervention study, profiling colonic mucosal transcriptome before and after FMT or placebo to identify molecular correlates of remission. machine-written summary
160 samples · 160 runs · Age unknown · 2018 · 63.2 Mbp / sample · cohort Fungal Trans-kingdom Dynamics Linked to Responsive
One study deposited as 3 BioProjects (746 catalog samples together): PRJEB26472 · PRJEB26473 · PRJEB26474 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 318 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 320 sample values (health condition, health condition detail) · PMC10965925, PMC8647676 |
| ○ 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 |
intervention — arms not resolved
Faecal microbiota transplantation design randomized_controlled_trial · population ulcerative_colitis · FMT vs placebo in active ulcerative colitis (FOCUS trial)
“randomised, controlled FOCUS Study of FMT” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
66 of 70 people sampled more than once (155 samples; median 2, up to 3 per person). Schedule stated by the source: “Samples at screening, week8_end_of_tx, end_of_open_label, or withdrawal_open_label_sae for patients in the FOCUS FMT/placebo trial.” (time origin: intervention start).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 160 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 160 | 100% | 160 | |||
| subject_id | 159 | 99% | 159 | |||
| health_condition_detail | 160 | 100% | 160 | |||
| timepoint_label | 159 | 99% | 159 |
- Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice. 2024 PMID 38531874 PMC10965925 own_data
- Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. 2020 PMID 32298656 PMC8647676 unsure
Archive description
Faecal Microbiota Transplantation (FMT) effectively induces remission in ulcerative colitis (UC). In the randomised, controlled FOCUS Study of FMT in active UC we aimed to identify bacterial taxonomic and functional determinants of therapeutic outcome.
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 study.title · “ulcerative colitis in the randomised, controlled FOCUS Study”
- body site study.title · “biopsy cDNA”
- body site study.description · “Faecal Microbiota Transplantation (FMT) effectively induces remission”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4705014 | health_condition | ulcerative_colitis | R3 | 0.70 | paper.fulltext.methods | Patients with UC were previously enrolled in a double-blind |
| SAMEA4705014 | health_condition_detail | Patients with UC (ulcerative colitis) enrolled in FMT trial | R3 | 0.70 | paper.fulltext.methods | Patients with UC were previously enrolled in a double-blind |
| SAMEA4705014 | subject_id | 1001 | R1 | 0.70 | sample.name_rule:sample_alias | C1-1001-Screening_S1_L001 |
| SAMEA4705014 | timepoint_label | screening | R1 | 0.70 | sample.name_rule:sample_alias | C1-1001-Screening_S1_L001 |
Sequencing
160 runs over 160 samples · mean 65.9 Mbp per run (median 63.2 Mbp, total 10.55 Gbp; 160 runs with a base count) · layout PAIRED 160 · platform ILLUMINA 160 · models Illumina MiSeq (160) · 0% of runs with a Sandpiper profile · first public 2018-12-18
Authors (18)
Leonardi I first · Paramsothy S · Doron I · Semon A · Kaakoush NO · Clemente JC · Faith JJ · Borody TJ · Mitchell HM · Colombel JF · Kamm MA · Iliev ID last · Luu LDW first · Pandey A · Ngo C · Castaño-Rodríguez N · Liu C · Man SM
Downloads
PRJEB26473.csv.gz (4.6 KB) · parquet (75.2 KB) — all 160 samples, every field with route and confidence · PRJEB26473_determinations.csv.gz (6.5 KB) — 638 evidence rows