 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 09, 2018 |
| Title |
Microbiome characterization using transfer RNA sequencing |
| Organisms |
Escherichia coli; Staphylococcus aureus; Bacillus subtilis; Barnesiella viscericola; mouse gut metagenome |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Here we report a direct tRNA sequencing protocol and software to simultaneously examine the composition and biological activity of naturally occurring microbial communities. Our analysis of mouse gut microbiome with tRNA-seq and 16S ribosomal RNA gene amplicons revealed comparable microbial community structures, and additional physiological insights into the microbiome through tRNA abundance and modifications.
|
| |
|
| Overall design |
Comprehensive analysis of high throughput sequencing data to determine microbial community structures in mouse gut microbiome (tRNA profiling dataset).
|
| |
|
| Contributor(s) |
Schwartz MH, Cui S, Clark WC, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Chang EB, Pan T, Eren AM |
| Citation(s) |
30559359 |
| Submission date |
Jun 20, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Tao Pan |
| E-mail(s) |
taopan@uchicago.edu
|
| Phone |
(773) 702-4179
|
| Organization name |
University of Chicago
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
929 E. 57th Street
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (6)
|
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
| GPL17443 |
Illumina HiSeq 2000 (mouse gut metagenome) |
| GPL17452 |
Illumina HiSeq 2000 (Staphylococcus aureus) |
| GPL18561 |
Illumina HiSeq 2000 (Bacillus subtilis) |
| GPL21051 |
Illumina MiSeq (mouse gut metagenome) |
| GPL25293 |
Illumina HiSeq 2000 (Barnesiella viscericola) |
|
| Samples (28)
|
| GSM2676377 |
C57BL/6 Gut Microbiome with Low Fat Diet, DM, Mouse1 |
| GSM2676378 |
C57BL/6 Gut Microbiome with Low Fat Diet, Mouse1 |
| GSM2676379 |
C57BL/6 Gut Microbiome with Low Fat Diet, DM, Mouse2 |
| GSM2676380 |
C57BL/6 Gut Microbiome with Low Fat Diet, Mouse2 |
| GSM2676381 |
C57BL/6 Gut Microbiome with Low Fat Diet, DM, Mouse3 |
| GSM2676382 |
C57BL/6 Gut Microbiome with Low Fat Diet, Mouse3 |
| GSM2676383 |
C57BL/6 Gut Microbiome with High Fat Diet, DM, Mouse1 |
| GSM2676384 |
C57BL/6 Gut Microbiome with High Fat Diet, Mouse1 |
| GSM2676385 |
C57BL/6 Gut Microbiome with High Fat Diet, DM, Mouse2 |
| GSM2676386 |
C57BL/6 Gut Microbiome with High Fat Diet, Mouse2 |
| GSM2676387 |
C57BL/6 Gut Microbiome with High Fat Diet, DM, Mouse3 |
| GSM2676388 |
C57BL/6 Gut Microbiome with High Fat Diet, Mouse3 |
| GSM3258497 |
E. coli culture, replicate 1 |
| GSM3258498 |
E. coli culture, replicate 2 |
| GSM3258499 |
E. coli culture, replicate 3 |
| GSM3258500 |
E. coli culture, DM, replicate 1 |
| GSM3258501 |
E. coli culture, DM, replicate 2 |
| GSM3258502 |
E. coli culture, DM, replicate 3 |
| GSM3258503 |
Barnesiella viscericola, replicate 1 |
| GSM3258504 |
Barnesiella viscericola, replicate 2 |
| GSM3258505 |
Staphylococcus aureus, replicate 1 |
| GSM3258506 |
Staphylococcus aureus, replicate 2 |
| GSM3258507 |
Staphylococcus aureus, replicate 3 |
| GSM3258508 |
Bacillus subtilis, replicate 1 |
| GSM3258509 |
Staphylococcus aureus, DM, replicate 2 |
| GSM3258510 |
Staphylococcus aureus, DM, replicate 3 |
| GSM3258511 |
Bacillus subtilis, DM, replicate 1 |
| GSM3258512 |
Bacillus subtilis, DM, replicate 2 |
|
| Relations |
| BioProject |
PRJNA391174 |
| SRA |
SRP109828 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100263_BSub_Counts.xlsx |
13.2 Kb |
(ftp)(http) |
XLSX |
| GSE100263_BV_tRNA_Counts.xlsx |
12.1 Kb |
(ftp)(http) |
XLSX |
| GSE100263_Ecoli_K12_tRNA_Counts.xlsx |
33.2 Kb |
(ftp)(http) |
XLSX |
| GSE100263_RAW.tar |
53.0 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE100263_StaphAureusCount.xlsx |
13.7 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...