|
| Status |
Public on Aug 11, 2019 |
| Title |
LN229/EGFRvIII+roscovitine IP |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: stable expression of EGFRvIII
cell line: LN229
cell type: glioblastoma
tissue: brain
antibody: anti-macroH2A1 antibody (07-219, Millipore)
treatment: 20 uM roscovitine
|
| Treatment protocol |
LN229 cells with stable expression of EGFRvIII were treated with vehicle (0.1% DMSO), erlotinib (10 μM) or Roscovitine (20 μM) for 16 h.
|
| Growth protocol |
LN229 glioma cells were maintained in 10% FBS/DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LN229 cells were cross-linked with formaldehyde to a final concentration of 1%. ChIP samples were prepared as described previously [(Buschbeck et al. The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat Struct Mol Biol 16, 1074-1079 (2009)].Immunoprecipitations were performed using 1μg anti- macroH2A1 antibody (07-219, Millipore) or the relevant non-specific IgG (Santa Cruz).
ChIP-seq libraries generation were performed according to standard protocols using BioScientific’s DNA Sample Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 5bp bin in the genome
Genome_build: hg19
|
| |
|
| Submission date |
May 09, 2019 |
| Last update date |
Aug 13, 2019 |
| Contact name |
Haizhong Feng |
| E-mail(s) |
fenghaizhong@sjtu.edu.cn
|
| Phone |
862168383921
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
Ren Ji Hospital
|
| Street address |
Pujian Road 160
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200127 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE130949 |
CDK5-dependent phosphorylation and nuclear translocation of TRIM59 promotes macroH2A1 ubiquitination and tumorigenicity |
|
| Relations |
| BioSample |
SAMN11609524 |
| SRA |
SRX5811245 |
