|
| Status |
Public on Jul 30, 2012 |
| Title |
IgG-ChIP-Seq-Control |
| Sample type |
SRA |
| |
|
| Source name |
NSCs & pOLs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: eNSCs & p2-pOLs
passage: eNSCs: 2-3 & p2-pOLs: 0
chip antibody: IgG (isotypic control antibody) [Abcam; Cat. no.: ab46540]
|
| 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 IgG control
|
| 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 |
|
| Relations |
| SRA |
SRX093165 |
| BioSample |
SAMN00714093 |
