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Sample GSM2364542 Query DataSets for GSM2364542
Status Public on Jan 12, 2017
Title SEM_MLL_Replicate_ChIPSeq
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
chip antibody: MLL1 (Bethyl, A300-086A)
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
 
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
E-mail(s) thomas.milne@imm.ox.ac.uk
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.
Relations
BioSample SAMN05951173
SRA SRX2281247

Supplementary file Size Download File type/resource
GSM2364542_SEM_MLL_Rep1_Peaks.bed.gz 157.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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