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Sample GSM4339188 Query DataSets for GSM4339188
Status Public on Nov 23, 2021
Title Sp6-mesenchyme
Sample type SRA
 
Source name dental mesenchyme
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: dental mesenchyme
chip antibody: Sp6 antibody (in house)
Extracted molecule genomic DNA
Extraction protocol Dental epithelium and mesenchyme samples from 30 newborn C57BL/6 P1 molars was isolated. After crosslinking with PFA, and sonication, Sp6 antibody was used for DNA immunoprecipitation.
DNA sequencing libraries were prepared by Active Motif and sequenced using an Illumina Genome Analyzer 2.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing 36 nt 5’- single-end sequencing reads were obtained using an Illumina Genome Analyzer II.
ChIP-seq reads were aligned to the mouse mm9 genome assembly using the ELAND algorithm
Only reads that map uniquely, have no more than two mismatches and pass quality control Q filtering were used. The reads were extended in silico using Active Motif TM software at their 3´-ends to a length of 130 bp.
BAR files were obtained by dividing the genome into into 32-nt bins and determining the number of reads (density) in each bin.
BED files were obtained from MACS files. The MACS (version 1.3.7.1) with a cutoff of p value <10e-7, band width of 130, and model fold of 12 was used to identify peaks.
Xlsx files contain Sp6 ChIP peaks within 10,000 bases of a known gene MGSC (build 37)
BAR files were obtained dividing the genome into into 32-nt bins and determining the number of reads (density) in each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bar files and Bed files can be viewed in Integrated Genome Browser (IGB)
Xlsx files contain Sp6 ChIP peaks within 10,000 bases of a known gene MGSC (build 37)
 
Submission date Feb 25, 2020
Last update date Nov 23, 2021
Contact name Yasuo Yoshitomi
E-mail(s) yositomi@icloud.com
Organization name NIH
Department NIDCR
Street address 30 Convent Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL9250
Series (1)
GSE145909 Genome-wide Analysis of Sp6/Epiprofin DNA Binding Sites in the Developing Mouse Molar Using ChIP-seq Analysis
Relations
BioSample SAMN14206867
SRA SRX7800519

Supplementary file Size Download File type/resource
GSM4339188_1_Mes_Sp6_intvl.bed.gz 132.8 Kb (ftp)(http) BED
GSM4339188_1_Mesenchyme_Sp6_s_1_norm_signal.bar.gz 133.6 Mb (ftp)(http) BAR
GSM4339188_Sp6_Mesenchyme_Excel.xlsx 930.6 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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