NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2121290 Query DataSets for GSM2121290
Status Public on Apr 28, 2016
Title POB_Sp7Ab-ChIP
Sample type SRA
 
Source name Primary osteoblasts
Organism Mus musculus
Characteristics cell type: Calvarial osteoblasts
age: P1
strain: C57BL/6
genotype: wild-type
chip antibody: Sp7 antibody (Abcam, catalog #ab22552, lot# GR193738-1)
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 Sp7 antibody ChIP-seq
Data processing DNA-sequence information was aligned to the unmasked mouse genome reference sequence mm9 by bowtie 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 Apr 13, 2016
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)
GSE76187 Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification
GSE80231 Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification [ChIP-Seq 2]
Relations
BioSample SAMN04849617
SRA SRX1702412

Supplementary file Size Download File type/resource
GSM2121290_POB_Sp7Ab-ChIP_peaks.bed.gz 4.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap