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Sample GSM6107491 Query DataSets for GSM6107491
Status Public on Sep 21, 2023
Title Mouse gut feces, TVA diet (zr4773_3V3V4)
Sample type SRA
 
Source name feces
Organism feces metagenome
Characteristics source: Mouse
rna population: 16S rRNA
treatment: TVA diet
tissue: feces
Extracted molecule genomic DNA
Extraction protocol ZymoBIOMICS®-96 MagBead DNA Kit (Zymo Research, Irvine, CA) was used to extract DNA using an automated platform.
Bacterial 16S ribosomal RNA gene targeted sequencing was performed using the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). In most cases, the bacterial 16S primers amplified the V3-V4 region of the 16S rRNA gene. 
The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation®(Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). The sequencing was performed with 10% PhiX spike-in.
Unique amplicon sequences variants were inferred from raw reads using the DADA2 pipeline
Taxonomy assignment was performed using Uclust from Qiime v.1.9.1 with the Zymo Research Database, a 16S database that is internally designed and curated
Composition visualization, alpha-diversity, and beta-diversity analyses were performed with Qiime v.1.9.1
Assembly: Zymo Research Database, a 16S database that is internally designed and curated
Supplementary files format and content: tab-delimited text files include taxonomy abundance for each Sample
 
Submission date May 05, 2022
Last update date Sep 21, 2023
Contact name fan hao
E-mail(s) haofan@uchicago.edu
Organization name University of Chicago
Street address 5801 S Ellis Ave
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL24937
Series (2)
GSE202266 Effect of trans-vaccenic acid(TVA) diet on 16S ribosomal RNA (rRNA) expression of mouse gut microbiome
GSE202340 Dietary trans-vaccenic acid promotes anti-tumor immunity
Relations
BioSample SAMN28099242
SRA SRX15161139

Supplementary file Size Download File type/resource
GSM6107491_zr4773_3V3V4.txt.gz 2.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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