|
| Status |
Public on Jul 01, 2018 |
| Title |
KO-2_FAT Tissue |
| Sample type |
SRA |
| |
|
| Source name |
Mice Subcutaenous Fat Tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Subcutenous Fat
age: post natal weeks 24
genotype: MKRN1 KO
gender: male
|
| Treatment protocol |
6 weeks old male mice fed high fat diet for 19 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Removed mice tissues were lysed with ice cooled trizol reagent and total RNAs were isolated.
RNA libraries were prepared with preprocessCore' R guide kit protocol (Part # 15026495)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Preprocessed reads were matched to reference genome sequence using HISAT2 program and then aligned reads were generated.
StringTie program was used for transcript assambly.
Expression levels were normalized with length of transcript and depth of coverage.
Expression profile data was exported by normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Differentially expressed transcripts included in two or more groups were selected through statistical verification.
In case that the genomic information was known, functional annotation and gene-set enrichment analysis were performed on the basis of GO and KEGG database.
Using SAMTOOLS & BCFTOOLS, variant calling was performed.
Fusion genes were predicted using defuse program.
Genome_build: UCSC mm10
|
| |
|
| Submission date |
May 29, 2018 |
| Last update date |
Jul 01, 2018 |
| Contact name |
Jae whan Song |
| E-mail(s) |
jso678@yonsei.ac.kr
|
| Organization name |
College of Life Science and Biotechnology
|
| Department |
Department of Biochemistry
|
| Street address |
Yonsei-ro 50
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE115012 |
RNA sequencing analysis of metabolism related genes in MKRN1-null mice tissues. |
|
| Relations |
| BioSample |
SAMN09274621 |
| SRA |
SRX4135603 |
