|
| Status |
Public on Jul 01, 2020 |
| Title |
Mkx_KO_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
tail tendon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tail tendon
strain: C57BL/6
genotype: Mkx-/-
age: 3-week-old
chip antibody: H3K27ac (Abcam, ab4729)
|
| Growth protocol |
Tail tendons were obtained from WT and Mkx-/- mice and cut into small pieces, and washed three times with PBS. The tissue fragments were digested with 0.2% collagenase (Life technologies) for 2hours at 37°C. The digest was centrifuged, and the pellet was suspended in Dulbecco’s modified Eagle’s medium (DMEM, low glucose; Gibco) with 10% (v/v) fetal bovine serum (FBS; Invitrogen) and 1% (v/v) penicillin-streptomycin (Gibco). At 100% confluence, cells were harvest for ChIP-seq experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit(E7645) following manufacture instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing reads were mapped to the mm9 genome with Bowtie by allowing up to two mismatches and keeping only uniquely mapped reads. PCR duplicated reads were removed with SAMtools.
H3K27ac ChIPseq peaks were identified with MACS version 2.1.0.
Defined H3K27ac peaks were then annotated to the mm9 genome with the Homer
Genome_build: mm9
|
| |
|
| Submission date |
Aug 22, 2017 |
| Last update date |
Jul 01, 2020 |
| Contact name |
HONGWEI OUYANG |
| E-mail(s) |
hwoy@zju.edu.cn
|
| Phone |
13958108337
|
| Organization name |
Zhejiang University
|
| Street address |
866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE102925 |
Epigenetic Analysis of Wild Type and Mkx-/- Tendon by Next Generation Sequencing |
| GSE102931 |
Alteration of transcriptomic and epigenetic landscapes in normal and heterotopic ossified tendons |
|
| Relations |
| BioSample |
SAMN07533400 |
| SRA |
SRX3111004 |
