|
| Status |
Public on May 31, 2024 |
| Title |
Colon tissue, MG_2, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
WT C57BL/6J with DSS water
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
strain: C57BL/6J
genotype: WT
disease state: induced acute colitis
treatment: high-dose of MG (200 mg/kg)
|
| Treatment protocol |
Mice were randomly divided into 6 groups with 10 mice per group: the untreated normal control, model group, low-dose MG group (50 mg/kg), medium-dose MG group (100 mg/kg), high-dose MG group (200 mg/kg) and SASP-positive group (500 mg/kg) that were orally administered once daily for 6 days.
|
| Growth protocol |
Acute colitis was induced in mice via administration of 2.5% (w/v) DSS in drinking water. Mice received either regular drinking water (normal group) or 2.5% DSS drinking water (model group and treatment groups) for 8 days followed by regular drinking water for 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA from colon tissues and RAW264.7 cells on the basis of the instructions of the manufacturer. Single-stranded cDNA was reverse transcribed from RNA by a reverse transcription kit (Vazyme Biotech, China)
The RNA-seq transcriptome library was prepared following the TruSeqTM RNA Sample Preparation Kit from Illumina using 1 μg of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA quality was determined by 2100 Bioanalyser (Agilent, USA) and quantified using the Nanodrop2000
After being quantified by TBS380, the paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2×150 bp read length)
functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P values ≤ 0.05 compared with the whole-transcriptome background
|
| |
|
| Submission date |
Oct 24, 2022 |
| Last update date |
May 31, 2024 |
| Contact name |
Lai Jia |
| E-mail(s) |
laijiazoe@126.com
|
| Organization name |
Southwest Medical University
|
| Street address |
Xianglin Road
|
| City |
Luzhou |
| ZIP/Postal code |
646000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE216434 |
Methyl Gallate Alleviates Acute Ulcerative Colitis by Modu-lating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway [RNA-seq] |
| GSE216435 |
Methyl Gallate Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway |
|
| Relations |
| BioSample |
SAMN31428394 |
| SRA |
SRX18006426 |
