|
| Status |
Public on Jan 23, 2018 |
| Title |
TCF7L2_Wntup_1 |
| Sample type |
SRA |
| |
|
| Source name |
cardiac ventricles
|
| Organism |
Mus musculus |
| Characteristics |
genotype: alphaMHC Cre recombinase positive, beta-catenin exon3 deleted-stabilized beta-catenin (transgenic)
strain: C57BL/6
chip-seq antibody: anti-TCF7L2 (17-10109, Millipore)
|
| 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 |
15 weeks-old adult murine cardiac ventricles; mice were kept on a 12/12 light/dark facility with ad lib access to food.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each IP, ventricles from atleast two murine hearts were pooled, washed in PBS, minced finely and fixed in 1.3% Formaldehyde for 20 min. The nuclei from tissue extracts were sonicated for 45 cycles to obtain the fragmented chromatin. Chromatin extracts containing DNA fragments with an average size of 300 bp were immunoprecipitated using 2µg/IP of different antibodies.
ChIP-seq library preparation was performed using NEBNext Ultra DNA library prep kit for Illumina (E7370) as per manual’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
QC was performed using FastQC v.0.10.0
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6.2 with default configurations.
peaks were called using MACS2 version 2.1.1.20160309.0. with the following settings: min. FDR-value (0.5), "Do not build shifting model", Arbitrary extension size (125bp).
noise peaks were filtered using mm9-blacklist from ENCODE.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph and files were generated using MACS2. Narrowpeaks and Broadpeaks were called on TCF7L2 and H3K27ac bound regions respectively. RPKM normalized bigwigs were generated using bamCoverage in Galaxy deepTools platform with default settings.
|
| |
|
| Submission date |
Apr 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Laura C Zelarayan |
| E-mail(s) |
laura.zelarayan@med.uni-goettingen.de
|
| 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 |
GPL17021 |
| Series (2) |
| GSE97761 |
A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart [ChIP-seq] |
| GSE97763 |
A context-specific cardiac Beta-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart |
|
| Relations |
| BioSample |
SAMN06754480 |
| SRA |
SRX2734776 |
