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GEO help: Mouse over screen elements for information. |
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Status |
Public on Sep 21, 2023 |
Title |
Mouse gut feces, TVA diet (zr4773_4V3V4) |
Sample type |
SRA |
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Source name |
feces
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Organism |
feces metagenome |
Characteristics |
source: Mouse rna population: 16S rRNA treatment: TVA diet tissue: feces
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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).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
May 05, 2022 |
Last update date |
Sep 21, 2023 |
Contact name |
fan hao |
E-mail(s) |
haofan@uchicago.edu
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Organization name |
University of Chicago
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Street address |
5801 S Ellis Ave
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City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60637 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN28099241 |
SRA |
SRX15161140 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6107492_zr4773_4V3V4.txt.gz |
2.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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