|
| Status |
Public on Sep 03, 2013 |
| Title |
GBC 5mC |
| Sample type |
SRA |
| |
|
| Source name |
Neurog1-EGFP positive cells
|
| Organism |
Mus musculus |
| Characteristics |
age: 4 weeks
tissue: main olfactory epithelium
cell type: Neurog1-EGFP positive cells
ip antibody: anti-5mC antibody (Active Motif)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using DNeasy (Qiagen) according to manufacturers instructions.
Libraries were constructed from gDNA samples by sonication to 200-1000 bp, end repair (NEB End Repair Kit), terminal A addition (Klenow), and Illumina adaptor ligation (NEB Quick Ligase). Samples were then immunoprecipitated with the indicated antibodies and amplified for 12-15 cycles
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
gDNA immunoprecipitated with anti-5mC antibody (Active Motif)
|
| Data processing |
Alignment: Samples were aligned using either Bowtie (DIP) or Tophat (mRNA) keeping only reads that matched uniquely to the mouse genome (mm9). Wig:
Wig: Values are the average number of reads within a given 200 bp window normalized by the library size in millions of reads.
FPKM tracking: Aligned mRNA samples were assembled to the UCSC refGene GTF using Cufflinks with bias correction against the mouse genome (mm9) and multi-read correction.
Genome_build: mm9
Supplementary_files_format_and_content: WIG
|
| |
|
| Submission date |
Jun 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Brainard |
| E-mail(s) |
msb@phy.ucsf.edu
|
| Organization name |
University of California, San Francisco
|
| Street address |
675 Nelson Rising Ln
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE38604 |
The developmental patterning of 5-hydroxymethylcytosine during neuronal differentiation |
|
| Relations |
| SRA |
SRX152552 |
| BioSample |
SAMN01041891 |
