|
Status |
Public on Nov 29, 2011 |
Title |
TKO2_H3K36me2_rep2 |
Sample type |
SRA |
|
|
Source name |
TKO2_H3K36me2_rep2
|
Organism |
Homo sapiens |
Characteristics |
cell line: TKO2 tissue type: blood genotype/variation: t(4;14)-associated NSD2 allele knocked-out 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 |
Lauring J et al. Blood. 2008 Jan 15; 111 (2): 856-64.
|
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.
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|
|
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 |
SRX063291 |
BioSample |
SAMN00618998 |
Named Annotation |
GSM721531_TKO2_H3K36me2_rep2.wig.gz |