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Sample GSM2364549 Query DataSets for GSM2364549
Status Public on Jan 12, 2017
Title SEM_siMLL-AF4_InputDNA
Sample type SRA
Source name Leukemia cell line (SEM)
Organism Homo sapiens
Characteristics cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
Growth protocol SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated (~200bp) and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description cells were treated with 300pmol MLL-AF4-specific siRNA
Data processing ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk
Submission date Oct 28, 2016
Last update date May 15, 2019
Contact name Thomas Milne
Organization name Weatherall Institute of Molecular Medicine
Department Molecular Haematology Unit
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL18573
Series (1)
GSE83671 MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.
BioSample SAMN05951183
SRA SRX2281254

Supplementary file Size Download File type/resource 277.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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