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Sample GSM2405924 Query DataSets for GSM2405924
Status Public on Feb 23, 2017
Title mv411_DMSO_6h_CDK9_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 6 hr
sequencing barcode: GGCACAAC
antibody: CDK9
antibody manufacturer: Santa Cruz
antibody catalog number: sc-484
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 CDK9
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 SAMN06054369
SRA SRX2375362

Supplementary file Size Download File type/resource
GSM2405924_mv411_DMSO_6h_CDK9_Rx.wig.gz 117.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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