|
| Status |
Public on Jul 31, 2013 |
| Title |
DNA methylation in 8 week sperm (replicate#1) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Methylated-CpG island recovery assay (MIRA) DNA from 8-week-old male sperm
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CF1 x TgOG2
cell type: sperm
gender: male
age: 8 weeks
mira: MBD3L1 and MBD2b
epigenetic feature: DNA methylation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryos and fetus gonads using a MoFlo or Aria II flow cytometer. For chromatin immunoprecipitation, cells were crosslinked before sorting. Chromatin from 400,000 cells was used for one ChIP using various antibodies. For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify ChIP- and MIRA-enriched DNA.
|
| Label |
Cy5
|
| Label protocol |
According to the standard NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
Input DNA from 8 week sperm
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: CF1 x TgOG2
cell type: sperm
gender: male
age: 8 weeks
mira: none
epigenetic feature: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GFP+ germ cells and GFP- gonadal somatic cells were flow sorted based on Oct4 promoter-driven EGFP expression in germ cells from CF1XOG2 embryos and fetus gonads using a MoFlo or Aria II flow cytometer. For chromatin immunoprecipitation, cells were crosslinked before sorting. Chromatin from 400,000 cells was used for one ChIP using various antibodies. For MIRA, the methylated fraction of sonicated genomic DNA from germ cells and sperm was captured using recombinant MBD3L1 and MBD2b proteins. Ligation-mediated PCR (LM-PCR) was performed to amplify ChIP- and MIRA-enriched DNA.
|
| Label |
Cy3
|
| Label protocol |
According to the standard NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
According to the NimbleGen Kit.
|
| Scan protocol |
Follow NimbleScan's default using the Agilent Scanner.
|
| Description |
MIRA_Sperm
Mice: CF1 (Charles River) females were mated with TgOG2 males (Szabo PE et al. Mech. Dev. 2002).
|
| Data processing |
Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction.
|
| |
|
| Submission date |
Apr 06, 2013 |
| Last update date |
Jul 31, 2013 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16978 |
| Series (2) |
| GSE45836 |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation (ChIP-chip and MIRA-chip) |
| GSE46954 |
Default DNA Methylation is Preceded by Broad, Low-Level Transcription in Fetal Male Germ Cells and Is Inversely Patterned by Dynamic H3K4 Methylation |
|
