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Sample GSM1600024 Query DataSets for GSM1600024
Status Public on Mar 11, 2015
Title H2AK119Ub MiG-empty ChIP-seq rep2
Sample type SRA
 
Source name H2AK119Ub MiG-empty ChIP-seq
Organism Mus musculus
Characteristics cell line: EML
tissue: bone marrow
cell type: basophil
atcc catalog number: CRL-11691
chip antibody: H2AK119Ub (Cell Signaling Technologies (Danvers, MA), Cat# 8240)
Biomaterial provider ATCC
Treatment protocol EML cells were transduced with either MSCV-IRES-GFP (MiG-empty) or with retroviral constructs encoding ASXL1(1-479) + BAP1 and expanded for 15 days post-transduction
Growth protocol EML cells cultured under conditions recommended by ATCC. ATCC Cat # CRL-11691
Extracted molecule genomic DNA
Extraction protocol IP's for ChIP-seq were carried out on mono-nucleosomes generated from EML cells.
ChiP-seq libraries were constructed using NEB's ChIP-seq library preparation kit for SOLiD sequencing.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB 5500xl Genetic Analyzer
 
Description processed data file: peaks_H2AK119Ub.bed
Data processing ChIP-seq reads were aligned using Bowtie (version 0.12.8), allowing only uniquely mapping reads, fragment sizes of 90-250bp, and removing duplicates.
Enriched areas were called using SICER with parameters as suggested in the documentation and for H2AK119Ub with win size=800 and gap size=2400.
Genome_build: mm9
Supplementary_files_format_and_content: BED files with SICER calls, DESeq result file, eXpress result files
 
Submission date Feb 03, 2015
Last update date May 15, 2019
Contact name Anjana Rao
E-mail(s) arao@liai.orgo
Organization name La Jolla Institute for Allergy and Immunology
Department Department of Signaling and Gene Expression
Street address 9420 Athena Circle
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL15907
Series (1)
GSE65555 Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex
Relations
BioSample SAMN03326192
SRA SRX864145

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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