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Sample GSM1976253 Query DataSets for GSM1976253
Status Public on Apr 28, 2016
Title MC3_Dlx5-FLAG1
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: FLAG M2 antibody (Sigma, F1804)
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 FLAG_ChIP-seq
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) hojo@tetrapod.t.u-tokyo.ac.jp
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 SAMN04357057
SRA SRX1492984

Supplementary file Size Download File type/resource
GSM1976253_MC3_Dlx5-FLAG1_peaks.bed.gz 279.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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