|
| Status |
Public on Jan 31, 2024 |
| Title |
PBS_3 |
| Sample type |
SRA |
| |
|
| Source name |
Small intestine
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Small intestine
genotype: WT
treatment: PBS
|
| Treatment protocol |
GF 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 tissue was harvested.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from whole SI tissue was isolated using the Qiagen RNeasy® Mini Kit (Qiagen 74104)
Libraries were prepared for sequencing using the NEB Ultra II Directional RNA Library Prep kit with Poly A isolation module
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Annotation, mapping and counting of the resulted reads were analyzed by SALMON with default parameters
LEfSe followed by multiple hypotheses correction using signal-to-noise rate and false discovery rate analyses was used to discover genes with differential abundance. Differences at LEfSe p < 0.05 and FDR < 0.05 were considered significant.
Assembly: GRCm38
Supplementary files format and content: xlsx containing Salmon output (TPM and fold change calculations)
|
| |
|
| 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 |
GPL24247 |
| Series (2) |
| GSE248692 |
Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells III |
| GSE248694 |
Gut bacteria-derived serotonin promotes immune tolerance in early life through regulation of neonatal gut T cells |
|
| Relations |
| BioSample |
SAMN38458385 |
| SRA |
SRX22659270 |
