|
| Status |
Public on Sep 30, 2015 |
| Title |
ck15r1am4 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: KLF15 KO
|
| Growth protocol |
Male C57BL/6J at 11-12 weeks of age were housed in 12 hour light-12 dark conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from apex of the heart using Trizol (Life technology) followed with miRNeasy Kit (Qiagen).
1ug of total RNA from each sample was depleted of ribosomal RNAs using Ribo-Zero. Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation kit. 100 bp paired-end sequencing was performed on pooled libraries in groups of three using an Illumina Hiseq 2500 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ck15_fpkm.txt
|
| Data processing |
Illumina reads were mapped to mouse genome release mm10 using GSNAP program. Reads mapped to single location in mm10 genome were retained for further analysis.
The raw read counts for each gene in mm10 RefSeq annotation were generated using HTSeq program. The expression levels of genes were presented as FPKM (fragments per kilo bases of exon per million of mapped reads) values.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mukesh Jain |
| E-mail(s) |
lxz99@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Case Cardiovascular Research Institute
|
| Street address |
2103 Cornell Road, Room 4537
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE63243 |
KLF15 Establishes the Landscape of Circadian Expression in the Heart |
|
| Relations |
| BioSample |
SAMN03177734 |
| SRA |
SRX758414 |
