|
| Status |
Public on Jan 31, 2024 |
| Title |
5HT_Col_1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon luminal contents
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon luminal contents
genotype: WT
treatment: 5HT
|
| 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 |
SAMN38458357 |
| SRA |
SRX22659246 |
