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Sample GSM3523531 Query DataSets for GSM3523531
Status Public on Sep 30, 2020
Title PA-1_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 SAMN10620402
SRA SRX5169915

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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