 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 20, 2021 |
| Title |
KMGS10 |
| Sample type |
SRA |
| |
|
| Source name |
Stool
|
| Organism |
human feces metagenome |
| Characteristics |
source: Human
rna population: 16s rRNA
patient diagnosis: NAFLD-
|
| Treatment protocol |
DNA extraction was carried out as described previously (doi: 10.1038/ismej.2014.250. Epub 2015 Jan 9), with few modifications, from 0.2g of stool sample that was mechanically lysed with 2.8mm ceramic beads (Mo Bio Laboratories Carlsbad, CA) and 0.1mm glass beads (Mo Bio Laboratories, Carlsbad, CA) for 2 cycles of 3 minutes at 3000rpm with a 45 seconds delay between cycles in 800μl of 200mM of monobasic NaPO4 (pH=8) and 100μl of guanidinium thiocyanate buffer. Samples were further centrifuged at 13,500g for 5 minutes and processed using the MagMAX-96 DNA Multi-sample kit (Life Technologies, Carlsbad, CA) via the MagMAX Express 96-Deep Well Magnetic Particle Processor (Applied Biosystems, Foster City, CA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified DNA was used for amplification of the 16S rRNA gene using paired end reads of the V3 region. Amplification of the bacterial 16S rRNA gene for the germ-free mice microbiota was done for the V3-V4 region. 50 ng of DNA was used as template with 1U of Taq, 1x buffer, 1.5 mM MgCl2, 0.4 mg/mL BSA, 0.2 mM dNTPs, and 5 pmoles each of 341F (CCTACGGGAGGCAGCAG) and 518R (ATTACCGCGGCTGCTGG) Illumina adapted primers, as previously described (doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1). The reaction was carried out at 94◦C for 5 minutes, 25 cycles of 94◦C for 30 seconds, 50◦C for 30 seconds and 72◦C for 30 seconds, with a final extension of 72◦C for 10 minutes. PCR products were then visualized on a 1.5% agarose gel. Positive amplicons were normalized using the SequalPrep Normalization Plate kit (Thermo Fisher, Wlatham, Massachusetts, USA).
custom amplicon
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
ASV_humans_updated.csv
|
| Data processing |
Library strategy: 16S rRNA-seq
BaseCalling on the MiSeq uses software called "RTA" v1.18.54.
For demultiplexing and FastQ generation: "bcl2fastq2" v2.20; allow 0 index mismatches for 16S data. After the bcl2 program from the sequencing facility we 1) trim the primers using Cutadapt, 2) error correct using dada2, 3) classify ASVs using SILVA version 132
Genome_build: The data were trimmed of adapters and denoised using dada2
Supplementary_files_format_and_content: .CSV files contain ASV counts.
|
| |
|
| Submission date |
Dec 03, 2020 |
| Last update date |
Sep 20, 2021 |
| Contact name |
Katherine Morrison |
| Organization name |
McMaster
|
| Street address |
1280 Main street west
|
| City |
Hamilton |
| ZIP/Postal code |
L8S 4L8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL29470 |
| Series (1) |
| GSE162608 |
Lower brown adipose tissue activity is associated with non-alcoholic fatty liver disease but not changes in the gut microbiota |
|
| Relations |
| BioSample |
SAMN16988408 |
| SRA |
SRX9626696 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
