|
| Status |
Public on Apr 28, 2016 |
| Title |
MC3_input2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro cultured osteoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: osteoblastic cell line MC3T3-E1
protocol: cultured for 1 week in osteogenic medium
chip antibody: none (input)
passages: 5-10
|
| Treatment protocol |
In in vitro culture, osteogenic media contained 10% FBS/alpha-MEM supplemented with 50 ug/mL ascorbic acid phosphate, 10 mM b-glycerophosphate and 10 ng/ml recombinant human BMP‑2 (rhBMP-2, 355-BM, R&D)
|
| Growth protocol |
Primary osteoblasts were isolated from P1 calvaria. In vitro cultured osteoblasts were isolated from MC3T3E1 cells cultured for 1 week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were isolated by 1 unit/ml Liberase TM (05401119001, Roche), Protein-DNA complexes were crosslinked with 1% formaldehyde, Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified with FLAG antibody.
Libraries were prepared ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics) according to manufacturer’s instruction
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
input DNA
This is used for peak calling for MC3_Sp1-FLAG1, MC3_Sp1-FLAG2, MC3_Sp7mut-FLAG1 and MC3_Sp7mut-FLAG2
|
| Data processing |
DNA-sequence information was aligned to the unmasked mouse genome build 37 by the ELAND aligner
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control
Genome_build: mm9
Supplementary_files_format_and_content: .bed file reports peaks
|
| |
|
| Submission date |
Dec 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hironori Hojo |
| E-mail(s) |
[email protected]
|
| Phone |
+81-3-5841-1427
|
| Organization name |
The University of Tokyo
|
| Department |
Center for Disease Biology and Integrative Medicine
|
| Lab |
Clinical Biotechnology
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE76185 |
Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification [ChIP-Seq] |
| GSE76187 |
Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification |
|
| Relations |
| BioSample |
SAMN04357098 |
| SRA |
SRX1492992 |
