|
| Status |
Public on Mar 08, 2019 |
| Title |
Tw2_DM_Ty1_20 |
| Sample type |
SRA |
| |
|
| Source name |
Twist2+ Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary myoblast
culture media: Growth Media
mouse genotype: Twist2-CreERT2; tdTO
|
| Treatment protocol |
Twist2+ cells were retrovirally infected with either 3xTy1-Twist2 or GFP
|
| Growth protocol |
Twist2+ cells were isolated from hind limb of Twist2-CreERT2;tdTO mice treated with 3 doses of Tamoxifen via FACS sorting. Cells were cultured on matrigel in Ham's F10, 20% FBS, 0.2%% Primocin, and 5 ng/ml of basic fibroblast growth factor prior to infection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked and fragment genomic DNA was extracted using the ChIP-IT Highsensitivity Kit from Active Motif
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the GRCh38/mm10 genome assembly using default parameters in BWA v0.7.12,
The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 1.3 and Sambamba version 0.6.6.
For E-box motif analysis,relaxed peaks were called using MACS version 2.1.0 with a p-value of 1x10-2 for H3K27ac and H3K27me3 and SPP version 1.4 with an IDR = 0.01 for each other sample
For PCA, differential peak analysis, peaks were called using HOMER version 4.7. For MyoD, Twist peaks were called using findpeaks command with with '-sytle factor' and FDR set to 1e-7. For histone marker ChIP-Seq data, peaks were called by findpeaks command with parameter ‘–style histone’ and other parameters set as default.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: HOMER peak files
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Stephen Li |
| E-mail(s) |
stephen.li@utsouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Molecular Biology
|
| Lab |
Olson Lab
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE127998 |
Genome-wide maps of Twist2-binding, MyoD-binding and chromatin state in Twist2-overexpressing Twist2+ cells |
|
| Relations |
| BioSample |
SAMN11082392 |
| SRA |
SRX5491841 |
