|
| Status |
Public on Sep 01, 2014 |
| Title |
TKO_H3K36me3_ChIPseq_1 |
| Sample type |
SRA |
| |
|
| Source name |
Multiple myeloma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Multiple myeloma
phenotype: Low levels of MMSET
passage: 15-20
chip antibody: Abcam ab9050
antibody lot #: 741327
|
| Growth protocol |
Cells were grown in RPMI1640 supplemented with 10% FBS and 1% Pen/Strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was performed according to the manufacture's protocol (ChIP kit, Millipore) with the following modifications: 107 cells were used per sample. After cell lysis, extracts were subjected to sonication with a 60 Sonic Dismembrator (Fisher Scientific) at 4°C for 20 cycles, cycling ON for 20 seconds and OFF for 1 minute at 4.5 power leading to a DNA average size of 200 bp. Immunoprecipitations were performed overnight at 4°C using 5 μg of antibody. Imunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit (QIAGEN).
10 ng of input and ChIP material was processed using the Illumina kit (IP-102-1001)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using Casava version 1.7
All samples were aligned to human genome (hg19) using bowtie 1
Several reads mapping to the same exact location were considered amplification artifacts and were excluded from the analysis.
The read density tracks were made using the HOMER tool (using default parameters), where each sample was normalized into 10 million reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
May 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Relja Popovic |
| E-mail(s) |
r-popovic@northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 East Superior Street
|
| City |
Chicago |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57977 |
MMSET Induces Global and Focal Changes in Histone Methylation in Myeloma Cells |
|
| Relations |
| BioSample |
SAMN02799815 |
| SRA |
SRX553426 |
