|
| Status |
Public on Jun 03, 2010 |
| Title |
Gli1FLAG GNP Chip |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Gli1-FLAG ChIP DNA from P8 RosaGli1-FLAG;Math1Cre granule neuron precusors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: RosaGli1-FLAG;Math1Cre
age: P8
tissue: normal cerebellum
cell type: granule neuron precursors
antibody: FLAG M2 mouse monoclonal
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
For GNPs, RosaGli1-FLAG c/c mice were crossed with Math1Cre mice and litters were taken at P8. Cerebellum was dissected into PBS and granule neuron precursor cells were isolated as previously described (Wechsler-Reya and Scott 1999). Medulloblastoma tumors were isolated from RosaGli1-FLAG c/c;Ptc+/- mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly isolated GNPs or tumor cells were then cross-linked with 1% formaldehyde for 30 minutes. ChIP and LMPCR was performed as previously described (Vokes et al., 2007). Prior to hybridization on promoter arrays, enrichment was verified by qPCR.
|
| Label |
biotin
|
| Label protocol |
Samples (5-7.5 ug DNA) were fragmented and biotin-labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| Channel 2 |
| Source name |
Total chromatin input from P8 RosaGli1-FLAG;Math1Cre granule neuron precursors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: RosaGli1-FLAG;Math1Cre
age: P8
tissue: normal cerebellum
cell type: granule neuron precursors
antibody: none
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
For GNPs, RosaGli1-FLAG c/c mice were crossed with Math1Cre mice and litters were taken at P8. Cerebellum was dissected into PBS and granule neuron precursor cells were isolated as previously described (Wechsler-Reya and Scott 1999). Medulloblastoma tumors were isolated from RosaGli1-FLAG c/c;Ptc+/- mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly isolated GNPs or tumor cells were then cross-linked with 1% formaldehyde for 30 minutes. ChIP and LMPCR was performed as previously described (Vokes et al., 2007). Prior to hybridization on promoter arrays, enrichment was verified by qPCR.
|
| Label |
biotin
|
| Label protocol |
Samples (5-7.5 ug DNA) were fragmented and biotin-labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| |
| Hybridization protocol |
At least 5 ug DNA was hybridzed per array using GeneChip Hybridization, Wash, and Stain kit (Affymetrix).
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Gli1-FLAG GNP ChIP biological replicates 1, 2, 3.
The RosaGli1FLAG mice were reported by Vokes et al., Development. 2007 May;134(10):1977-89.
The Math1-Cre mice were reported by Matei et al., Dev Dyn. 2005 Nov;234(3):633-50.
|
| Data processing |
Data was quantile normalized and analyzed with TileMap. Log2(IP/Input) fold changes (fc) for each probe, and TileMap moving average (ma) statistics for each probe, are reported in the BAR files. fc.bar and ma.bar are generated by CisGenome software (previously TileMap). The high-confidence binding regions reported in the paper are listed in the 'Gli1FLAG_GNP_Chip.bed' and 'Gli1FLAG_MB_Chip.bed' files.
|
| |
|
| Submission date |
Aug 17, 2009 |
| Last update date |
Jun 03, 2010 |
| Contact name |
Eunice Lee |
| Organization name |
Stanford University
|
| Department |
Developmental Biology
|
| Lab |
Matthew Scott
|
| Street address |
318 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL5811 |
| Series (2) |
| GSE17682 |
Chromatin localization of Gli1 in granule neuron precursor cells and medulloblastoma |
| GSE17719 |
Gli1 regulatory networks in granule neuron precursor and medulloblastoma cells |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM441165_Gli1FLAG_GNP_Chip.fc.bar.gz |
23.8 Mb |
(ftp)(http) |
BAR |
| GSM441165_Gli1FLAG_GNP_Chip.ma.bar.gz |
22.8 Mb |
(ftp)(http) |
BAR |
| GSM441165_Gli1FLAG_GNP_Chip1_042307_PromPR.CEL.gz |
19.2 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_Chip2_050407_PromPR.CEL.gz |
19.1 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_Chip3_080207_PromPR.CEL.gz |
17.6 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_Input1_042307_PromPR.CEL.gz |
19.6 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_Input2_050407_PromPR.CEL.gz |
18.9 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_Input3_080207_PromPR.CEL.gz |
18.0 Mb |
(ftp)(http) |
CEL |
| GSM441165_Gli1FLAG_GNP_chip.bed.gz |
15.5 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
