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Sample GSM786030 Query DataSets for GSM786030
Status Public on Jul 30, 2012
Title Ezh2-ChIP-Seq-NSCs
Sample type SRA
Source name Neural stem cells (NSCs)
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Embyonic (E14) neural stem cells (eNSCs)
passage: 2-3 (cultured as neurospheres)
chip antibody: Anti Ezh2 [Diagenode (; Cat. no.: CS-039-100; Lot no.: 001]
Growth protocol NSCs were cultured in T25 (Nunc, Roskilde) tissue culture flasks containing proliferation medium, consisting of Neurobasal medium supplemented with 2% B27, human recombinant epidermal growth factor (EGF; 20ng/ml), and basic fibroblast growth factor (bFGF; 20ng/ml). Pre-myelinating oligodendrocytes were cultured in standard SATO medium.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. DNA was precipitated using Phenol/chloroform/IAA method. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (IP-102-1001) Following the instructions on the kit "A" bases were added to the 3' End of the DNA fragments and fragments were ligated to Adapters. Subsequently, the Adapter-Modified DNA fragments were run on a 2% agarose gel to generate the DNA libraries based on fragments length (200 +/-25bp). Finally the Adapter-Modified DNA fragment libraries were enriched by PCR. After validating (quality control) libraries by Bioanalyzer, the sequencing reactions were performed with system components and reagents on the Genome Analyzer following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Chromatin IP against Ezh2
Data processing Alignment: Sequence reads were obtained and mapped to the mm9 genomes using Bowtie for Illumina software. Maximum number of mismatches permitted 2
Submission date Aug 25, 2011
Last update date May 15, 2019
Contact name Falak Sher
Organization name CHB
Department F.M. Kirby Neurobiology Center
Street address 3 Blackfan Circle, CLs 12220 Center for Life Science Building
City Boston
State/province MA
ZIP/Postal code MA 02115
Country USA
Platform ID GPL11002
Series (1)
GSE31655 Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes
SRA SRX093163
BioSample SAMN00714091

Supplementary file Size Download File type/resource
GSM786030_fsher-Ezh2-ChIP-Seq-NSCs.bam 198.7 Mb (ftp)(http) BAM 71.3 Mb (ftp)(http) BW
GSM786030_fsher-Ezh2-ChIP-Seq-NSCs.wig.gz 15.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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