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Sample GSM913292 Query DataSets for GSM913292
Status Public on May 13, 2013
Title ChIP_RBPj_1F1_C2C12_6hDelta_repl2
Sample type SRA
 
Source name C2C12, Delta 6h, RBP-J 1F1 ChIP
Organism Mus musculus
Characteristics cell line: C2C12
treatment: Delta 6h
technique: ChIP-sequencing
chip antibody: anti-RBP-J 1F1 rat monoclonal
antibody vendor/provider: Ascenion
Treatment protocol Delta treatments: For ligand-dependent activation of Notch signaling, cells were grown in the presence of the extracellular domain of Delta-like 1 fused to the Fc fragment of human IgG (Hicks et al., 2002) (kindly provided by N. Gupta upon permission from G. Weinmaster). Culture dishes were first coated with 10 µg/ml anti-Fc antibody for 1h at RT. Dishes were then incubated with conditioned medium from transfected 293T cells expressing the fusion proteins, for 1h at RT. C2C12 cells were plated in fresh medium and grown for 6h or 24h on the immobilized-ligand containing dishes.
Growth protocol C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen) at 37 °C in 5% CO2 atmosphere.
Extracted molecule genomic DNA
Extraction protocol Cells were trypsinized according to standard procedures. A cell suspension with cell density of 5 million/ml was made in cell medium. Cells were subsequently cross-linked for 30 min at RT in medium plus 1% formaldehyde and 1/14 volume of buffer A (0.1M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM HEPES pH7.6), quenched with 0.125 M glycine and washed at 4°C with the following buffers: (i) PBS, (ii) buffer B: 0.25% Triton-X-100, 10mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, (iii) buffer C: 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50 mM HEPES pH7.6. During each washing step, cells were rotated for 10 min at 4°C and subsequently centrifuged for 7 min at 500g 4°C. Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton-X-100, 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, 1x protease inhibitor cocktail complete (Roche)) at 20 million/ml and sheared using a Bioruptor (Diagenode) with the following settings: high power, 30s on/off, 18 cycles. Sonicated chromatin was centrifuged for 5 min at 13000 rpm in eppendorf tubes, supernatant was snap-freezed in liquid nitrogen and stored at -80 °C or directly used in ChIPs. For one ChIP, 100 µl chromatin was incubated with 2 µg antibody, 20 µl 50% protein A/G bead (Santa Cruz), in 1x ChIP incubation buffer with 0.1% BSA in a total volume of 300 µl o/n at 4°C. Beads were then washed with the following buffers: twice with buffer1: 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, 0.15M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, once with buffer2: 0.1% SDS, 0.1% NaDOC, 1% Triton-X-100, 0.5M NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, once with buffer3: 0.25M LiCl, 0.5% NaDOC, 0.5% NP-40, 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6, and twice with buffer4: 1mM EDTA pH8, 0.5mM EGTA pH8, 20mM HEPES pH7.6. During each washing step, beads were rotated for 5 min at 4°C and subsequently centrifuged for 2 min at 4000 rpm 4°C. Precipitated chromatin was then eluted from beads in 200 µl elution buffer (1% SDS, 0.1M NaHCO3) for 40 min at RT. Materials (precipitated chromatin or input chromatin in elution buffer) were decross-linked for 5h at 65 °C with addition of 200 mM NaCl. DNA was purified on QIAquick spin columns according to QIAGEN protocols. For sequencing, 6-8 ChIPs were pooled.
1 to 20 ng was used for library preparation using the ChIP-seq DNA sample Prep Kit (Illumina, cat# IP-102–1001) using the recommended protocol. After ligation of adapters, a 300 bp band is excised using the E-Gel system (Invitrogen), which correspond to a 234 bp fragment of genomic DNA. PCR enrichment of adapter-ligated DNA was done using 14 cycles of PCR.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Mouse myoblast cell line (established from thigh muscle from an adult C3H strain female).
Data processing ChIP-seq: Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the mouse (mm9) reference genome using the Illumina Analysis Pipeline, allowing one mismatch. Only the tags uniquely aligning to the genome were considered for further analysis. Duplicated reads were discarded to obtain a non-redundant set. Further analysis was performed using the 36 bp sequence reads. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Mus musculus mm9 genome assembly.
Genome_build: mm9
 
Submission date Apr 11, 2012
Last update date May 15, 2019
Contact name Arjen Brinkman
E-mail(s) arjen.brinkman@gmail.com
Organization name Radboud University, Nijmegen Center for Molecular Life Sciences
Department Molecular Biology
Lab Stunnenberg
Street address NCMLS #274, Geert Grooteplein Zuid 30
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
 
Platform ID GPL11002
Series (1)
GSE37184 Dynamic binding of RBPJ is determined by Notch signalling status
Relations
SRA SRX140337
BioSample SAMN00854797

Supplementary file Size Download File type/resource
GSM913292_ChIP_RBPj_1F1_C2C12_6hDelta_repl2.reads.bed.gz 135.5 Mb (ftp)(http) BED
GSM913292_ChIP_RBPj_1F1_C2C12_6hDelta_repl2.wig.gz 42.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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