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Sample GSM687284 Query DataSets for GSM687284
Status Public on Jan 03, 2012
Title mES_Mi-2b
Sample type SRA
 
Source name Embyonic stem cells
Organism Mus musculus
Characteristics chip antibody: Mi-2b
antibody catalog number: Abcam AB72418
antibody lot number: GR3133-1
cell type: V6.5 embryonic stem cells
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against Mi2-b
Data processing Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
See Supplemental Information of associated manuscript for details regarding generation of WIGs.
 
Submission date Mar 08, 2011
Last update date May 15, 2019
Contact name Richard A Young
E-mail young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9250
Series (2)
GSE27841 Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq)
GSE27844 Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation
Relations
SRA SRX047143
BioSample SAMN00217287

Supplementary file Size Download File type/resource
GSM687284_12092010_62T5DAAXX_B4.ylf.gz 31.8 Mb (ftp)(http) YLF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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