GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM845242 Query DataSets for GSM845242
Status Public on Jan 03, 2012
Title H3K4me1 C646 rep1
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics chip antibody: H3K4me1
chip antibody manufacturer: Abcam
chip antibody catalog number: AB8895
cell line: V6.5 embryonic stem cells
drug: C-646
concentration: 30uM
time: 24hours
replicate: 1
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 HiSeq 2000
Description Chromatin IP against H3K4me1 in C646 treated cells- ChIPSeq replicate 1
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.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Submission date Dec 07, 2011
Last update date May 15, 2019
Contact name Richard A Young
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 GPL13112
Series (2)
GSE27841 Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation (ChIP-seq)
GSE27844 Enhancer Decommissioning by LSD1 During Embryonic Stem Cell Differentiation
SRA SRX110647
BioSample SAMN00764089

Supplementary file Size Download File type/resource
GSM845242_09282011_C039RACXX_3.ACAGTG.wig.gz 167.2 Mb (ftp)(http) WIG
GSM845242_09282011_C039RACXX_3.ACAGTG.ylf.gz 43.7 Mb (ftp)(http) YLF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap