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Sample GSM7918817 Query DataSets for GSM7918817
Status Public on Jan 31, 2024
Title PBS_SI_5
Sample type SRA
 
Source name Small intestine luminal contents
Organism Mus musculus
Characteristics tissue: Small intestine luminal contents
genotype: WT
treatment: PBS
Treatment protocol WT neonatal mice were given 50 μL of 5-HT (12.5 μg/mL) or vehicle (PBS) at P8 and P9 via oral gavage. The mice were then sacrificed at P14 and SI and colon luminal contents were collected for 16S sequencing.
Extracted molecule genomic DNA
Extraction protocol Bacterial genomic DNA was extracted from luminal contents using the E.Z.N.A stool DNA kit (Omega Biotek)
The V4-V5 region within the 16S rRNA gene was amplified and prepared for sequencing using standard Illumina 16S Metagenomic Sequencing Library Preparation protocols
Other: 16S rRNA seq
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Data processing Paired-end reads were analyzed and classified into operational taxonomic units (OTUs) at > 97% identity level using Mothur v.1.35
Taxonomic assignments were determined using the SILVA 16S rRNA reference file release 132 and the Ribosomal Database Project (RDP) training set version 16
LEfSe Linear discriminant analysis (LDA) was performed by the Mothur command using all OTU reads
Assembly: SILVA 16S rRNA reference file release 132
Supplementary files format and content: OTU table xlsx file
 
Submission date Nov 27, 2023
Last update date Jan 31, 2024
Contact name Katherine Sanidad
E-mail(s) kzs4001@med.cornell.edu
Organization name Weill Cornell Medicine
Street address 413 E69th St
City New York
ZIP/Postal code 11365
Country USA
 
Platform ID GPL16417
Series (2)
GSE248691 Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells II
GSE248694 Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells
Relations
BioSample SAMN38458367
SRA SRX22659236

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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