|
| Status |
Public on Jan 05, 2017 |
| Title |
input DNA_WT_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rnf40+/+
passages: 3
chip antibody: none
|
| Treatment protocol |
For RNF40 knockout, MEFs were passaged into GlutaMAX™-DMEM supplemented with 250nM of 4-hydroxitamoxifen (4-OHT) for 5 days, and then cultured for 3 days without 4-OHT.
|
| Growth protocol |
Primary MEFs were cultured in high-glucose GlutaMAX™-DMEM (Invitrogen) supplemented with 10% FBS Superior (Biochrom), 1% penicillin–streptomycin (Sigma-Aldrich), and 1% non-essential amino acids (Invitrogen) at 37°C, 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0
peaks were called using MACS version 1.0.0 with the following setting: Effective Genome Size (Mouse (mm9)), Tag size (25), Bandwidth (300), Pvalue (0.00001), Shift size (125).
Coverage was determined by normalizing the filtered reads per hundred million
bigwig files were generated using Wig/BedGraph-to-bigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from wig files using Wig/BedGraph-to-bigWig
|
| |
|
| Submission date |
Aug 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A Johnsen |
| E-mail(s) |
steven.johnsen@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Clinic for General, Visceral and Pediatric Surgery
|
| Lab |
AG Tumorepigenetics
|
| Street address |
Robert Koch Strasse 40
|
| City |
Göttingen, Niedersachsen |
| State/province |
Niedersachsen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE72237 |
Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 [ChIP-Seq Data Set] |
| GSE72239 |
Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 |
|
| Relations |
| BioSample |
SAMN04003030 |
| SRA |
SRX1160454 |
