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Sample GSM2364551 Query DataSets for GSM2364551
Status Public on Jan 12, 2017
Title PT_AF4_ChIPseq
Sample type SRA
Source name L826
Organism Homo sapiens
Characteristics cell type: Presentation ALL patient sample engrafred in mice and harvested from spleen
chip antibody: AF4 (Abcam, ab31812)
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
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 SAMN05951179
SRA SRX2281256

Supplementary file Size Download File type/resource
GSM2364551_PT_AF4_Peaks.bed.gz 15.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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