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Sample GSM2212241 Query DataSets for GSM2212241
Status Public on Jan 12, 2017
Title SEM_Menin_ChIPSeq
Sample type SRA
 
Source name Leukemia cell line (SEM)
Organism Homo sapiens
Characteristics cell line: Leukemia cell line; SEM
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
chip antibody: Menin (Bethyl, A300-105A)
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; all other cell lines were grown in a similar manner in RPMI 1640.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
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
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR
 
Submission date Jun 23, 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 GPL11154
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 SAMN05290463
SRA SRX1873453

Supplementary file Size Download File type/resource
GSM2212241_SEM_Menin_Peaks.bed.gz 9.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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