Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer/Experiment 3

Reviewed Marked as Reviewed by Atrayees on 2023-8-18

Curated date: 2022/07/03

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Intestine Bowel,Intestinal tract,Intestine,intestine

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer

Group 0 name Corresponds to the control (unexposed) group for case-control studies: paracancerous tissue (pa2t)

Group 1 name Corresponds to the case (exposed) group for case-control studies: cancerous tissue (cat)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: 37-88 years of age, cancerous tissue. Note: Group 0 = paracancerous tissue 2-5 cm from cancerous tissue

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Sanger

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Matched on Factors on which subjects have been matched on in a case-control study: Matched on: "patient" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.patient