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PRJNA905672 SRP409946

Archaeome of tumor vs healthy mucosa, Tunisian CRC patients

Metagenomic data of gut microbiome from tunisian CRC patients

68 FFPE tissue samples (33 tumor, 35 healthy mucosa) from Tunisian colorectal cancer patients, analyzed by shotgun metagenomics in a case-control design to characterize gut archaeal communities, notably Halobacteria enrichment in tumor tissue. machine-written summary

68 samples · 68 runs · TN · Adult · 2023 · 0.24 Gbp / sample

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Sources
✓Sequence archive 542○Abstract / description✓Full text 136✓Supplementary tables 68–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive542 sample values (age, collection date, country, health condition, health condition detail, latitude, longitude, sex)
○ Abstract / descriptionread; no usable statement
✓ Full text136 sample values (location locality, location site) · PMC10527824
✓ Supplementary tables68 sample values (subject id)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance
1 sampling locations · 1 country
Age
elderly34
adult32
unknown2
Condition
healthy_control35
other_cancer33
Sex
female39
male29
Country
TN68
Body site
primary35
excluded33
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 7 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 36 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 18 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 6 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)all projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 0.24 Gbp per sample0130Gbp
Community composition
Clostridioides 21.1%Niallia 6.2%Caldimonas 4.9%not assigned to a genus 67.8%

Genera, mean relative abundance over 2 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category66 97%
country68 100%68
health_condition68 100%68
subject_id68 100%68
collection_date68 100%68
detailed_location68 100%
health_condition_detail68 100%68
latitude68 100%68
location_locality68 100%68
location_site68 100%68
longitude68 100%68
sex68 100%68
age_at_collection_days66 97%66
Papers (1)
Details
Archive description

Analysis of microbiome of tunisian colorectal cancer patients

How this project entered the registry

Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • body site study.title · “Metagenomic data of gut microbiome from tunisian”
  • body site study.description · “microbiome of tunisian colorectal cancer patients”
  • body site sample.attr.host_tissue_sampled · “tumor colorectal mucosa (n=33/68)”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage sample.attr.host_age · “64 (n=37/68)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN31880608age_at_collection_days23741.2R10.70sample.attr.host_age65
SAMN31880608collection_date2022-08R10.90biosample.attribute:collection_date2022-08
SAMN31880608countryTNR10.90sample.attr.geo_loc_nameTunisia
SAMN31880608health_conditionhealthy_controlR10.85biosample_attrhealthy mucosa
SAMN31880608health_condition_detailhealthy mucosaR10.90sample.attr.host_diseasehealthy mucosa
SAMN31880608latitude33.8869R10.90biosample.attribute:lat_lon33.8869 N 9.5375 E
SAMN31880608location_localitySfaxR30.70paper.fulltext.methodsHabib Bourguiba Hospital, Sfax, Tunisia
SAMN31880608location_siteHabib Bourguiba Hospital, Department of PathologyR30.70paper.fulltext.methodsbiobank of the Department of Pathology, Habib Bourguiba Hospital
SAMN31880608longitude9.5375R10.90biosample.attribute:lat_lon33.8869 N 9.5375 E
SAMN31880608sexfemaleR10.90sample.attr.host_sexfemale
SAMN31880608subject_id216R20.75paper.supp.cimb-45-00477-s001.zip/supplementary data S1.xlsx[samples characterisation!code patient]Mic001 | 216 (8) | healthy adjacent mucosa
Sequencing

68 runs over 68 samples · mean 0.36 Gbp per run (median 0.24 Gbp, total 24.70 Gbp; 68 runs with a base count) · layout PAIRED 68 · platform ILLUMINA 68 · models Illumina MiSeq (68) · 7% of runs with a Sandpiper profile · first public 2023-06-21 – 2023-06-22

Authors (9)

Mathlouthi NEH first · Oumarou Hama H · Belguith I · Charfi S · Boudawara T · Lagier JC · Ammar Keskes L · Grine G · Gdoura R last

Downloads

PRJNA905672.csv.gz (3.6 KB) · parquet (75.0 KB) — all 68 samples, every field with route and confidence · PRJNA905672_determinations.csv.gz (6.8 KB) — 746 evidence rows

Samples (68 · every field this project has values for · hover a cell for its source)
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