|
| Status |
Public on Dec 28, 2015 |
| Title |
forelimb buds Ring1b 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ChIP
|
| Organism |
Mus musculus |
| Characteristics |
tissue: forelimb buds
strain: BDF1
chip antibody: Ring1b
|
| Treatment protocol |
Whole forelimb buds at E10.5 from wild type embryos were fixed in 1% formaldehyde/PBS for 20 min at room temperature, washed three times with cold PBS containing protease inhibitors and stored at -80°C. Pools of forelimb buds were used for ChIP and it was performed as described previously (Endoh et al., 2012).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Antibodies against Ring1B (clone #3) (Atsuta et al., 2001) and H3K27me3 (07-449, Millipore) were used for immunoprecipitation. Purified immunoprecipitated and whole cell extract (input) DNA were amplified using the double-round T7 RNA polymerase-based amplification method (van Bakel et al., 2008).
|
| Label |
Cy3
|
| Label protocol |
Agilent Mammalian ChIP-on-chip Version 9.0, August 2006
|
| |
|
| Channel 2 |
| Source name |
input
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: input
tissue: forelimb buds
strain: BDF1
|
| Treatment protocol |
Whole forelimb buds at E10.5 from wild type embryos were fixed in 1% formaldehyde/PBS for 20 min at room temperature, washed three times with cold PBS containing protease inhibitors and stored at -80°C. Pools of forelimb buds were used for ChIP and it was performed as described previously (Endoh et al., 2012).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Antibodies against Ring1B (clone #3) (Atsuta et al., 2001) and H3K27me3 (07-449, Millipore) were used for immunoprecipitation. Purified immunoprecipitated and whole cell extract (input) DNA were amplified using the double-round T7 RNA polymerase-based amplification method (van Bakel et al., 2008).
|
| Label |
Cy5
|
| Label protocol |
Agilent Mammalian ChIP-on-chip Version 9.0, August 2006
|
| |
|
| |
| Hybridization protocol |
Agilent Mammalian ChIP-on-chip Version 9.0, August 2006
|
| Scan protocol |
Agilent Mammalian ChIP-on-chip Version 9.0, August 2006
|
| Data processing |
Signal intensities were normalized using rank consistency filter algorithm and Ring1b-binding genes and H3K27me3-positive genes were determined using enrichment index dependent on the maximum log(fold enrichment) of 500bp window around TSS (-4kb to +4kb). Since the index had two peaks, the group having higher scores were obtained with false discovery ratio 0.05.
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
Dec 28, 2015 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
[email protected]
|
| 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 |
GPL4129 |
| Series (2) |
| GSE70074 |
RING1 links retinoic acid signaling to the early proximal-distal specification of forelimb bud via Meis2 repression (ChIP-chip) |
| GSE70077 |
RING1 proteins contribute to early proximal-distal specification of the forelimb bud by restricting Meis2 expression |
|
