|
| Status |
Public on Feb 23, 2017 |
| Title |
mv411_DMSO_24h_Pol2_Rx |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF4 rearranged acute myeloid leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MV4;11(Cas9; ENL-FKBP(F36V); ENL-/-)
input: mv411_input_Rx
treatment: 0.01% DMSO for 24 hr
sequencing barcode: TAGTCGTG
antibody: RNA Pol II
antibody manufacturer: Diagenode
antibody catalog number: C15100055
|
| Treatment protocol |
ENL-FKBP(F36V) was degraded with addition of 500 nM dTAG-13 (final DMSO concentration of 0.01%). Control treatments were performed with 0.01% DMSO
|
| Growth protocol |
RPMI, 10% FBS
MV4;11 cells (obtained from the laboratory of Prof. Scott A. Armstrong) were cultured in RPMI supplemented with 10% FBS, penecillin, and streptomycin. ENL-FKBP(F36V)-expressing MV4;11 cells were selected with 2 µg/mL puromycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-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 |
Chromatin IP against RNA Pol II
|
| 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 |
Nov 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE82116 |
Transcription control by the ENL YEATS domain in acute leukemia [ChIP-seq] |
| GSE82118 |
Transcription control by the ENL YEATS domain in acute leukemia |
|
| Relations |
| BioSample |
SAMN06054372 |
| SRA |
SRX2375359 |
