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Sample GSM941548 Query DataSets for GSM941548
Status Public on Nov 27, 2012
Title input_AF4_HiSeq_ChIPSeq
Sample type SRA
 
Source name Acute lymphoblastic leukemia cells with MLL/AF4 translocation, input
Organism Homo sapiens
Characteristics cell type: RS4;11 ALL cells
chip antibody: none
Growth protocol The human RS4;11 ALL cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, CA) with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 100 μg/ml streptomycin.
Extracted molecule genomic DNA
Extraction protocol ChIP: For histone ChIP, RS4;11 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. For MLL and AF4 ChIP, RS4;11 cells were double-fixed with 2mM Disuccinimidyl Glutarate and then 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight, and after increasing stringency washes, immunocomplexes were recovered and DNA was isolated. The ChIP protocol in RS4;11 cells was followed as outlined in Milne et al. (PMID 19277579), using a formaldehyde fixation protocol for H3K79me2 and H3K4Me3, and a 45 minute, 2mMDSG and a 30 minute 1% double-fixation protocol for MLLN and AF4C.

Library construction: Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library Preparation Kit following the manufacturer's instructions (Illumina, CA). Briefly, 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Paired with the AF4 ChIP-seq.
Data processing Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.7 with default parameters. All 36-bp-long reads were mapped to the reference human genome sequence, hg18, using Illumina’s ELAND aligner with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277 (PMID 21736739)) and annotated to genes and/or promoters based on hg18 RefSeq genes downloaded from the UCSC Genome Browser.
Genome_build: hg18
Supplementary_files_format_and_content: BIGWIG: Counts.
Supplementary_files_format_and_content: BED: Peaks.
 
Submission date Jun 01, 2012
Last update date May 15, 2019
Contact name Huimin Geng
E-mail(s) huimin.geng@ucsf.edu
Organization name UCSF
Department Department of Laboratory Medicine
Street address 513 Parnassus Ave., MSB S-1480
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL11154
Series (2)
GSE34941 Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia
GSE38403 Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia [ChIP-seq]
Relations
SRA SRX151227
BioSample SAMN01001964
Named Annotation GSM941548_s_1_Input_AF4_HiSeq.nh.overlap.bigWIG

Supplementary file Size Download File type/resource
GSM941548_s_1_Input_AF4_HiSeq.nh.overlap.bigWIG 550.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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