|
| Status |
Public on Apr 26, 2017 |
| Title |
MM1S_E2F1 |
| Sample type |
SRA |
| |
|
| Source name |
Multiple Myeloma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MM1.S
input: MM1S_WCE_MUNSHI
treatment: none
barcode: N/A
antibody: anti E2F1
antibody maker: Cell Signaling
antibody catalog number: Cell Signaling #3742
|
| Growth protocol |
All MM cell lines were cultured in RPMI–1640 media containing 10% fetal bovine serum (FBS, GIBCO, Life technologies, Carlsbad, CA, United States), 2 mmol/L L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin (GIBCO, Life technologies, Carlsbad, CA, United States).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and chromatin-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-Seq for transcription factor E2F1 in MM1.S cells
|
| Data processing |
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format
|
| |
|
| Submission date |
Apr 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nikhil C Munshi |
| E-mail(s) |
nikhil_munshi@dfci.harvard.edu
|
| Phone |
617-632-4218
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Hematologic Oncology
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE80661 |
Non-overlapping control of transcriptome by Promoter and Super-Enhancer-Associated Dependencies |
|
| Relations |
| BioSample |
SAMN04901595 |
| SRA |
SRX1726515 |
