|
| Status |
Public on Jan 23, 2018 |
| Title |
Wntup_1 |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac ventricles
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 15 weeks-old
genotype: alphaMHC Cre recombinase positive, beta-catenin exon3 deleted-stabilized beta-catenin
|
| Treatment protocol |
12 weeks-old adult mice were administered with TX 30mg/Kg/day for 3 days and were sacrificed 3 weeks-post induction
|
| Growth protocol |
mice were kept on a 12/12 light/dark facility with ad lib access to food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from mice cardiac tissue using NucleoSpin RNA kit from Macherey-Nagel (Cat no: 740955.10). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1x50 bp; 51 cycles with single indexing; 6 GB ca. 30- 35 million reads per sample).
Sequence reads were aligned to the mouse reference assembly (UCSC version mm9) using Bowtie 2.0
For each gene, the number of mapped reads was counted using htseqcount and DESeq2 was used to analyze the differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Excel file contains the output from DESeq2: variance stabilized counts of the raw data (normalization).
|
| |
|
| Submission date |
Apr 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura C Zelarayan |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medical Center, Goettingen
|
| Department |
Institute of Pharmacology and Toxicology
|
| Street address |
Robert-Koch Strasse 40
|
| City |
Goettingen |
| State/province |
Lower Saxony |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE97762 |
A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart [RNA-eq] |
| GSE97763 |
A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart |
|
| Relations |
| Reanalyzed by |
GSM3431082 |
| BioSample |
SAMN06754465 |
| SRA |
SRX2734792 |
