Summary of Study ST000366

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000291. The data can be accessed directly via it's Project DOI: 10.21228/M8F600 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000366
Study TitleMetabolomics analysis of colon adenoma in African Americans
Study TypeMetabolomics
Study SummaryThis NMR Metabolomics analysis was performed on feces samples derived from healthy (n = 10) and adenoma (n = 10) African American subjects with the goal of identifying perturbations in metabolomics profiles in colon cancer.
Institute
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Num Groups2
Total Subjects20
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2017-07-10
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8F600
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000291
Project DOI:doi: 10.21228/M8F600
Project Title:Microbiomic analysis in African American with Colonic Lesions
Project Type:Microbiome
Project Summary:Increasing evidence suggests a role in colorectal carcinogenesis to the gut microbiota. However, no specific bacteria have been unequivocally linked to either initiation or progression of colorectal cancer (CRC). A Microbiome analysis was conducted to analyze the microbiota composition and functional potential in African Americans with colorectal lesions with the goal of detecting markers of diagnostic value. DNA from 10 CRC tumors and their matched normal tissues as well as stool samples from 10 colon adenomas and 10 healthy subjects were analyzed for their bacterial composition and genomic content. 16S rDNA amplicons were analyzed by HITChip 16S microarray and by sequencing in stool samples and colon tissues, respectively. The functional potential was determined by sequence-based metagenomics using Illumina at a depth of 15 million reads per tissue sample to compensate for the host’s DNA presence. For the stools, the metagenomic sequencing was performed at 3 million reads per sample. Metagenomic Linkage Groups (MLGs) were established and those with high discriminative power between healthy and neoplastic specimens were analyzed for their genetic content. Also, metagenomic reads from stool samples were mapped against bacterial genes from tissues and reads from tissues were mapped against stools assembled bacterial genes to identify common markers with discriminative power.
Institute:Howard University
Department:Department of Pathology and Cancer Center
Last Name:Brim
First Name:Hassan
Address:2041 Georgia Avenue, N.W., Washington, DC 20060
Email:hbrim@howard.edu
Phone:202-806-4198
Funding Source:NIH

Subject:

Subject ID:SU000387
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and Female
Human Race:African American
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Condition
SA016487CC0944Adenoma
SA016488CC0995Adenoma
SA016489CC0839Adenoma
SA016490CC0904Adenoma
SA016491CC0911Adenoma
SA016492CC0901Adenoma
SA016493CC0872Adenoma
SA016494CC0885Adenoma
SA016495CC0883Adenoma
SA016496CC0899Adenoma
SA016497CC0961Normal
SA016498CC0981Normal
SA016499CC0990Normal
SA016500CC0929Normal
SA016501CC01068Normal
SA016502CC0868Normal
SA016503CC0890Normal
SA016504CC0895Normal
SA016505CC0908Normal
SA016506CC0914Normal
Showing results 1 to 20 of 20

Collection:

Collection ID:CO000381
Collection Summary:None
Sample Type:Colon
Storage Conditions:-70C

Treatment:

Treatment ID:TR000401
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000394
Sampleprep Summary:Fecal samples (20 mg) were mixed with 1000 μL of D2O, mixed thoroughly by vortexing, and then centrifuged at 16000 x g for 20 min. The supernatants were removed and filtered through 0.22μ centrifuge filters at 16000 x g for 20 minutes. 540 μl of the filtrate was mixed with 60 μl of Chenomix Internal Standard mixture (containing DSS, Imidazole, and NaN3 in D2O). Aliquots of 550 μl were then transferred into 5mm NMR tubes.

Analysis:

Analysis ID:AN000599
Analysis Type:NMR
Num Factors:2

NMR:

NMR ID:NM000066
Analysis ID:AN000599
Instrument Name:Bruker950 MHz
Instrument Type:Other
NMR Experiment Type:Other
NMR Comments:nmr experiment type: noesypr1d
Field Frequency Lock:Deuterium
Standard Concentration:0.5 mM
Spectrometer Frequency:950 MHz
NMR Probe:5 mm ATMA Cryoprobe
NMR Solvent:D2O
NMR Tube Size:5mm, 7 inch
Shimming Method:Topshim
Pulse Sequence:noesypr1d
Water Suppression:yes
Pulse Width:8.44 us
Power Level:12.589 W
Receiver Gain:4
Offset Frequency:4471.1 Hz
Presaturation Power Level:0.00003588 W
Chemical Shift Ref Cpd:DSS
Temperature:298.1 K
Number Of Scans:256
Dummy Scans:4
Acquisition Time:1.075 s
Relaxation Delay:2 s
Spectral Width:16 ppm, 15.243 kHz
Num Data Points Acquired:32k
Real Data Points:32k
Line Broadening:0.5 Hz
Zero Filling:yes
Apodization:Lorentzian
Baseline Correction Method:Polynomial
Chemical Shift Ref Std:DSS
Binned Increment:0.04
Binned Data Excluded Range:4.68 - 4.88 (water)
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