|
| Status |
Public on Dec 26, 2014 |
| Title |
H3K4me3 1of2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: thymocytes
antibody: none (input)
|
| Treatment protocol |
Thymocytes were subjected to ChIP assay using anti-trimethyl-Histone H3 (Lys4) (07-473, Millipore), anti-trimethyl-Histone H3 (Lys27) (07-449, Millipore), and anti-Ring1B (D139-3, MBL) antibodies.
|
| Growth protocol |
Thymocytes were cultured in standard medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Purified immunoprecipitated and input DNA were subjected to blunt ligation with linker oligo DNA, linker-mediated PCR (LM-PCR), labeling, hybridization and washing following the Agilent mammalian ChIP-on-chip protocol.
|
| |
|
| Channel 2 |
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: thymocytes
antibody: anti-trimethyl-Histone H3 (Lys4) (07-473, Millipore)
|
| Treatment protocol |
Thymocytes were subjected to ChIP assay using anti-trimethyl-Histone H3 (Lys4) (07-473, Millipore), anti-trimethyl-Histone H3 (Lys27) (07-449, Millipore), and anti-Ring1B (D139-3, MBL) antibodies.
|
| Growth protocol |
Thymocytes were cultured in standard medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Purified immunoprecipitated and input DNA were subjected to blunt ligation with linker oligo DNA, linker-mediated PCR (LM-PCR), labeling, hybridization and washing following the Agilent mammalian ChIP-on-chip protocol.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
H3K4me3 ChIP-chip 1 of 2
|
| Data processing |
Cy5/Cy3 ratios were calculated and assigned to TSS (from 4kb upstream to 4kb downstream) of all genes using our in-house program. Means of log ratio were approximated with two Gaussian curves and marked genes were classified as FDR (false discovery ratio) was 0.05.
Processed data contain Yes/No classification of analysis described above.
|
| |
|
| Submission date |
Dec 26, 2013 |
| Last update date |
Dec 26, 2014 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14573 |
| Series (2) |
| GSE53649 |
ChIP-chip analysis of Ring1B in thymocytes |
| GSE53650 |
Ring1A and Ring1B in thymocytes |
|
