|
| Status |
Public on Sep 30, 2020 |
| Title |
PA-2_LP_ILC3 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: HR-1
milk-diet: PA-milk
cell type: Lamina propria ILC3s
|
| Treatment protocol |
Small intestine lymphocytes, ILC3s were isolated from two groups of mice at age of 18 weeks old: offspring mice that were breastfed with maternal milk with high amount of palmitic acid or normal group.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small intestine intraepithelial and lamina propria layer's lmphocytes were isolated via enzymatic treatment and percol gradient purification. ILC3s from IEL and LP were analyzed and sorted via FACSAria and RNA was harvested using Qiazol reagent. SMART-Seq v4 Ultra Low Input RNA Kit was used for the construction of sequencing libraries.
RNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for amplication and sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
The reads were mapped onto the reference mouse genome mm10 using TopHat ver.2.1.1 in combintaion with Bowtie ver.2.2.8.0 and SAMtools ver. 0.1.18.
Gene expression was quantified with Cufflinks ver.2.2.1. and Cuffdiff ver.2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Counts and FPKMs
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Sep 30, 2020 |
| Contact name |
masamoto kanno |
| E-mail(s) |
mkanno@hiroshima-u.ac.jp
|
| Phone |
+81-82-257-5175
|
| Organization name |
Hiroshima University
|
| Department |
Department of Immunology
|
| Street address |
1-2-3, kasumi, Minami-ku
|
| City |
Hiroshima |
| ZIP/Postal code |
734-8551 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE124182 |
Long-chain saturated fatty acids in breast milk are associated with the pathogenesis of atopic dermatitis via inducing inflammatory ILC3s |
|
| Relations |
| BioSample |
SAMN10620401 |
| SRA |
SRX5169916 |
