Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
Services Request Form: Center for Clinical and Translational Metagenomics
Please fill out relevant sections per experimental work to be undertaken. You may
indicate “pending” for IRB/IACUC/COMS protocols, as well as grant and charge-back
information. Core staff use this information to identify resources needed for projects, set
timelines, and generate quotes for services. Staff of the core will be in contact to discuss
specifics and help define best approaches.
Services requested: please check all areas that apply:
Microbiology
Gnotobiotic Mouse Facility
Molecular and Sequencing Services
Computational Services
A: Investigator Information:
Investigator: __________________ Phone: _____________
Email: ____________
Primary Contact: _______________ Phone: _____________
Email: ____________
Institutional Affiliation: _______________________
Funding Source: _________________
HDDC member:
Yes
No
Grant#:_____________________________
Peoplesoft# (Partners investigators)__________________________________________
Purchase Order# (for non-Partners investigators)_______________________________
Protocol information (if submitting human samples, requesting mice or isolates):
Human Research Studies:
IRB Protocol# ______________________ Expiration Date: _____________________
IRB Granting Institution: __________________________________________________
Animal Studies:
IACUC Protocol#: _____________ Expiration Date: ___________________________
IACUC Granting Institution: _______________________________________________
COMS/IBC Protocol#: ___________________ Expiration Date: __________________
(COMS = Committee on Microbiological Safety)
COMS Granting Institution: _______________________________________________
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 1
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
B.: Description of experiment (add additional pages as needed). Please include (1)
aims of experiment (2) source of materials to be submitted for analysis, (3) numbers of
biological replicates in each group, (4) desired analyses and (5) how data will be used.
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 2
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
C. Gnotobiotic services
Mouse strains to use:
BALB/c
C57BL/6
Swiss-Webster
Other: _____________________________________________________________
Source of mice:
CCTM bred
Taconic
UNC
Other: _____________________________________________________________
Biohazard level:
Procedures:
Gnotobiotic
BL-1
BL-2
Colonization/gavage
Blood collection
Gavage of non-microbial materials
IP injections
Fecal pellet collection
Weighing mice in isolators
Altered Diet (state desired diet(s): _______________________________________
___________________________________________________________________
Release GF mice to another facility (list the facility and contact): _______________
_____________________________________________________________________
Other: _____________________________________________________________
D. Samples to be submitted for microbiology, metagenomic or histopathology
Species from which materials will be obtained:
human
mouse
Other:______________________________________
Sample type(s): (check all that apply)
Stool
Whole blood
Stomach
Skin
Urine
Duodenum
Microbial Isolate
Sputum
Jejunum
Other:_______________________
Ileum
Cecum
Colon
Other: _____________________________________
Sampling method:
Fecal Pellet/Stool
Biopsy
Bowel – full thickness
Scraping
Swab
Other:____________________________________________________________
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 3
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
Environmental samples: ___________________________________________
How many samples will be submitted of each type (provide any additional description
regarding different sample sets across experiments or for specific types of analyses):
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
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© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
E. Analyses:
Microbiology
Qualitative culture – presence/absence of one or more species:
Please indicate species of interest: ________________________________
____________________________________________________________
Quantitative culture – counts only
Quantitative culture – speciation of isolates
Indicate if specific species should be isolated: ________________________
_____________________________________________________________
Other microbiological analyses: _________________________________
____________________________________________________________
Do you need stocks of isolates to be prepared from cultured materials?
Metabolic profiling
Short chain fatty acid analyses
Indicate sample type(s) for analysis
Pure isolates
Stool samples (human or mouse)
Cecal contents (mouse)
Other: _______________________
Biochemical typing of pure isolates
Indicate type of analysis desired for cultured isolates: __________________
_____________________________________________________________
Resistance testing of pure isolates
Indicate desired antibiotics to test: _________________________________
____________________________________________________________
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 5
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
Metagenomic and Genomic Analyses
Depending upon desired analyses, sample preparation may be undertaken in the CCTM
core lab or by the sequencing core providing services. Contact CCTM staff if you have
questions about options.
DNA extraction and QC
RNA extraction and QC
16S rRNA gene phylotyping and community structure analyses.
full-length 16S or 18/28S rRNA gene sequencing for typing (pure
bacterial or fungal isolates only).
Genome sequencing of pure isolates.
Please indicate any preferences for sequencing platform:
Illumina MiSeq (250bp paired-end; 16S V4 region, or limited metagenomic
whole shotgun reads from DNA or RNA)
Illumina HiSeq (Commonly 100-150bp paired-end; metagenomic WGS,
RNAseq)
Roche 454, Titanium Chemistry (300-400nc reads, cover 16S V1-V3 regions,
average of 10K reads/sample to aim for 5K/sample that are usable.
Other: ______________________________________________
Core facility for sequencing: For non-MiSeq applications, the CCTM collaborates with
Baylor’s Alkek Microbiome Center but also works with a number of area centers.
CCTM: MiSeq analyses
Baylor Genome Center (Roche 454 and Illumina; fee/service – charged per
sample submitted and desired # of reads/sample)
Broad Institute (Illumina platforms; requires prior agreement with the Broad
for services)
Tufts University Genome Center (Illumina HiSeq2000; fee/service - charged
per lane on flow cell or quotes issued per analyses performed.)
Other: ______________________________________________
Desired read depth/sample: requested average number of reads/sample. You may
speak with CCTM staff if uncertain regarding required depth for particular applications.
Avg. reads/sample: _____________________
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 6
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.
Center for Clinical and Translational Metagenomics, Request form, v 1.5
05/15/2014
Computational Analyses: Discussion with core staff is needed to identify the best
approaches for analyzing your metagenomics data. In addition to the general categories
below, please indicate desired use of data obtained from analyses.
Please briefly describe the data set to be collected and specific hypotheses to be tested.
If this is an exploratory project, please briefly describe what sorts of structure you expect
to find in the data.
Bioinformatics Analyses:
16S rRNA phyotyping - clustering to operational taxonomic units (OTU) with
taxonomic assignment, and number of counts/OTU.
Whole genome shotgun sequencing of complex communities - assignments
of reads to reference genomes or gene families/homologies
Genome sequencing of pure isolates: assembly of short reads into contigs,
basic genome annotation.
Other: _____________________________________________________
Statistical and Machine Learning Analyses:
Experimental design and power analysis
Prediction of host phenotype from microbial community structure
Testing differences among subgroups based on microbial community
structure
Integration of multiple data sources (e.g., immunological readouts with
microbiology results)
Relational/network analyses
Time-series analyses
Other: _____________________________________________________
Email to rkappa@partners.org or FAX to 617-264-6898, ATTN: CCTM
Page: 7
© 2014, Center for Clinical and Translational Metagenomics, Brigham & Women’s Hospital.
All rights reserved.