|
| Status |
Public on Nov 29, 2011 |
| Title |
KMS11_H3K36me2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
KMS11_H3K36me2_rep2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KMS11
tissue type: blood
genotype/variation: t(4;14)(q16.3;q32.3)
gender: Female
chip antibody: anti-H3K36me2
chip antibody vendor: Active Motif
chip antibody lot#: 308001
chip antibody catalog#: 39255
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the corresponding antibodies and protein A-conjugated magnetic beads (Invitrogen). Briefly, cells were cross-linked with 1% formaldehyde and lysed with the buffer containing 50mM Tris-HCl pH=8.0, 10mM EDTA, 1% SDS and protease inhibitors. Cell lysate was sonicated with Branson Digital Sonifier (Branson) and diluted with RIPA buffer by 10 fold (v/v) before incubated overnight with antibody-protein A-magnetic beads complexes. In the next day, beads were washed three times with RIPA buffer and twice with TE buffer. IP ed DNA was eluted from beads, de-crosslinked at 68 and purification by MinElute PCR Purification Kit (Qiagen). Purified DNA was subject to ChIP-sequencing analysis.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
N/A
|
| Data processing |
Reads are mapped to genome (hg18) using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-8, DANPOS is used to calculated ChIP intensity.
|
| |
|
| Submission date |
May 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
kaifu chen |
| E-mail(s) |
kaifuc@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor plaza, suite 450A
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE29146 |
NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [ChIP] |
| GSE29305 |
NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming |
|
| Relations |
| SRA |
SRX063288 |
| BioSample |
SAMN00618995 |
| Named Annotation |
GSM721528_KMS11_H3K36me2_rep2.wig.gz |
