|
| Status |
Public on Mar 05, 2013 |
| Title |
PGK12.1ES_PolIIS5p_genome tiling |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
PolIIS5p ChIP DNA from mouse female PGK12.1 ES cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Wild type XX
cell line: PGK12.1 ES
strain: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.
chip antibody: PolIIS5p
|
| Treatment protocol |
No treatment
|
| Growth protocol |
ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.
|
| Label |
Cy5
|
| Label protocol |
Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.
|
| |
|
| Channel 2 |
| Source name |
ChIP input DNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: input
antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.
|
| Label |
Cy3
|
| Label protocol |
Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.
|
| |
|
| |
| Hybridization protocol |
Standard NimbleGen protocol
|
| Scan protocol |
Standard NimbleGen protocol
|
| Description |
NimbleGen genome tiling array 2007-07-27_MM8_TILE_ChIP_10_HX1 was used.
|
| Data processing |
Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
Mar 05, 2013 |
| Contact name |
Xinxian Deng |
| E-mail(s) |
dengx2@u.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Laboratory Medicine and Pathology
|
| Lab |
HSB C526
|
| Street address |
1959 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL10129 |
| Series (2) |
| GSE30761 |
Mammalian X upregulation |
| GSE44835 |
Upregulation of the mammalian X chromosome is associated with enhanced transcription initiation, MOF-mediated H4K16 acetylation, and longer RNA half-life |
|
