|
| Status |
Public on Mar 22, 2016 |
| Title |
KO_UTX_Female |
| Sample type |
SRA |
| |
|
| Source name |
Satellite cells from muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6/129
genotype: UTX-Floxed, Pax7-CreER, Rosa26-Floxed-TdTomato
tissue: Differentiating Myoblasts
Sex: Female
|
| Treatment protocol |
Sorted TdT+ SCs from UTXmKO/TdT or UTXWT/TdT mice were induced to differentiate for 24 h.
|
| Growth protocol |
SCs from UTXmKO/TdT or UTXWT/TdT mice were grown in in Ham's F10 modified media supplemented with 20 % fetal calf serum, 4 mM L-Glutamine, 1.5 g/L sodium bicarbonate, 2.5 ng/mL of FGF, and 2.5 µM of 4-OH-Tamoxifen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then isolated using RNAesay kit (Qiagen) using an on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were initially mapped to the known mm9 transcripts (GTF file from the UCSC) using Bowtie version 2.2.4 / TopHat 2.0.12 using default values. Unmapped reads were then mapped to the mm9 genome.
Splice junctions were determined with TopHat version 2.0.12 using default values.
Transcript quantification was performed with Cufflinks version 2.2.1 and HT-Seq 0.6.1.
Identification of differentially expressed genes was performed with the CuffDiff from Cufflinks version 2.2.1 and EdgeR bioconductor package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the read per million mapped reads coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite (version 2.16.2) and UCSC genome browser standalone tools for Unix from the aligned reads output of TopHat version 2.0.12 using default values.
Supplementary_files_format_and_content: Text file contains quantification for each gene in Fragments Per Million Kilobase (FPKM).
|
| |
|
| Submission date |
Jun 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Marjorie Brand |
| E-mail(s) |
karthi.sivaraman@gmail.com, mbrand@ohri.ca
|
| Organization name |
Ottawa Hospital Research Institute
|
| Street address |
501 Smyth Road
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE69968 |
RNA-Sequencing of primary myoblasts from mice with a satellite cell specific knockout of the histone demthylase UTX/KDM6A |
|
| Relations |
| BioSample |
SAMN03780056 |
| SRA |
SRX1063697 |
