|
| Status |
Public on Dec 31, 2023 |
| Title |
Oxi-LA_10 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
genotype: Oxi-LA
strain: C57BL/6
molecule: 16S rRNA
|
| Treatment protocol |
The fecal samples were collected from un-oxidized or oxidized corn oil-treated mice.
|
| Growth protocol |
C57BL/6 male mice were fed with the diet containing un-oxidized or oxidized corn oil for 3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total fecal DNA was extracted using QIAamp DNA Stool Mini Kit (Qiagen) following the manufacturer’s instruction with the addition of bead-beating step.
PCR was performed to amplify the bacteria community with primers that bound the V3-4 regions of the16S rRNA gene,which also incorporates the Illumina overhang adaptor.PCRs were performed in a 96-well format on a Veriti thermal cycler (Life Technology) with 2 × KAPA HiFi Hotstart ReadyMix (KAPA Biosystem). After purification with AMPure XP beads (Beckman Coulter), a limited cycle PCR was performed using the Nextera XT Index Kit (Illumina) to attach dual indices and Illumina sequencing adapters, followed by an additional purification with AMPure XP bead. The quantity of the purified PCR products was measured by Qubit dsDNA BR Assay kit (Life Technology) and the amplicon quality was estimated by ScreenTape Assay on Tape Station 2200 (Agilent). After quantification and qualification, samples were pooled in equimolar amount and pair-end 2×300 bp sequencing was performed on Illumina MiSeq platform and MiSeq reagent kit V3 (8% PhiX) (Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
For all sequencing data, the raw reads were subject to quality check using FastQC.
The sequencing data was further trimmed and analyzed by QIIME software qiime2-2020.11.
Sequences were then clustered into operational taxonomic unites (OTUs) using a public dataset (SILVA release 132) with 99% similarity threshold.
QIIME2 output were imported to R to build a phyloseq project.
Differential abundance analysis in the polysome fraction was determine using AVONA.
Supplementary files format and content: tab-delimited text files include differential abundance analysis results
Library strategy: 16S rRNA-seq
|
| |
|
| Submission date |
Jul 22, 2022 |
| Last update date |
Dec 31, 2023 |
| Contact name |
RENHUA SONG |
| E-mail(s) |
Renhua.song1989@gmail.com
|
| Phone |
61452667663
|
| Organization name |
Centenary Institute
|
| Lab |
Epigenetics and RNA Biology Program
|
| Street address |
Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive
|
| City |
Camperdown |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE209580 |
Dietary fatty acids interact with gut microbiota and TLR4 to promote colitis and colorectal tumorigenesis |
|
| Relations |
| BioSample |
SAMN29903094 |
| SRA |
SRX16461994 |
