 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 12, 2019 |
| Title |
FVB/129P2 backcross 3 IgG ChIPseq, 2 |
| Sample type |
SRA |
| |
|
| Source name |
FVB/129P2 backcross 3
|
| 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 |
rep3.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 |
SAMN10846736 |
| SRA |
SRX5310585 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
