|
| Status |
Public on Aug 28, 2015 |
| Title |
OCI-LY7 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI-LY7
cell type: GCB-DLBCL
genotype: wt
stain: tumor
antibody: KMT2D antibody
|
| Treatment protocol |
1% formaldehyde for 10 min
|
| Growth protocol |
GCB-DLBCL cell lines were grown in IMDM with 15%FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared to 200-400bp, incubated with KMT2D antibody (in-house generated human KMT2D antibody specific for the N-terminus previously described in Hu D. et. al Mol Cell Biol 2013 PMID:24081332) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr. Final chormatin was purified using Qiagen PCR purification columns.
KAPA HTP ChIP-seq sample prep kit (KAPA Bioystems)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Peak calling were performed by ChIPseeqer-2.1 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: peak file is in .txt format
|
| |
|
| Submission date |
Mar 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanwen Jiang |
| E-mail(s) |
yaj2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
413 E. 69th St. BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE67314 |
MLL4 (KMT2D) inactivating mutations lead to focal loss of H3K4me1/2 and deregulated gene expression in B cell lymphomas |
|
| Relations |
| BioSample |
SAMN03450726 |
| SRA |
SRX971780 |
