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Sample GSM3583933 Query DataSets for GSM3583933
Status Public on Feb 12, 2019
Title FVB/129P2 backcross 1 IgG ChIPseq
Sample type SRA
 
Source name FVB/129P2 backcross 1
Organism Mus musculus
Characteristics strain: FVB/129P2 backcross
antibody: IgG
genotype/variation: Cdkn2ab
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% formaldehyde; 50mM Hepes-KOH; 100mM NaCl; 1 mM EDTA; 0,5 mM EGTA. Cell lysis was performed in LB1 buffer with final pH 7,5 (50 mM Hepes-KOH; 140mM NaCl; 1mM EDTA, 10% Glycerol, 0.5% NP-40; 0,25% Triton X-100; Proteinase inhibitor) for 20 minutes at 4°C. Subsequently, nuclei were lysed using LB2, pH 8,0 (10mM Tris-HCl; 200 mM NaCl; 1mM EDTA; 0,5mM EGTA; Proteinase inhibitor) for 10 minutes at 4°C. Pellets were resuspended in LB3 pH8,0 (10mM Tris-HCl; 100mM NaCl; 1 mM EDTA; 0,5mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine; Proteinase inhibitor). Crosslinked chromatin was sheared (400-800 bp) using a Covaris S2 with Tube and Caps (Covaris, 520048), using the following settings: duty cycle: 10%, intensity: 4, cycles per burst: 200 time 40 seconds with 20 cycles. Chromatin precipitation was performed overnight using antibody-bound (CTCF 5 l, SMC1 10 l, Igg 10 per IP) proteinA coupled DynaBeads (Invitrogen). Elution and decrosslinking was performed overnight at 65°C in EB pH 8,0 (50mM Tris-HCl; 10mM EDTA; 1% SDS). Samples were treated with Proteinase K and RNAseA for 2 hours. DNA was isolated using phenol extraction and ethanol precipitation.
Library preparation was done using a KAPA Library preparation kit using the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description rep1.narrowPeak
Data processing Reads were mapped to GRCm38 using bowtie2 with default settings.
Peak calling was performed using MACS2 (v2.1.1) (Feng et al., 2012) using IgG as control.
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeak
 
Submission date Jan 30, 2019
Last update date Feb 12, 2019
Contact name Robin H. van der Weide
Organization name Hubrecht Institute
Lab Kind Lab
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platform ID GPL17021
Series (1)
GSE125885 Natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis.
Relations
BioSample SAMN10846739
SRA SRX5310583

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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