|
| Status |
Public on Jan 05, 2011 |
| Title |
p73_ChIP_Rap_B |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
p73 ChIP DNA from Rh30, rapamycin
|
| Organism |
Homo sapiens |
| Characteristics |
cells: Rh30 rhabdomyosarcoma cells
treatment: 40 nM rapamycin
antibody: Bethyl A300-126A anti-p73
|
| Treatment protocol |
Rh30 cells were treated with vehicle or 40 nM rapamycin in serum-free media for 24 h.
|
| Growth protocol |
Cells were cultured in RPMI (Invitrogen) containing 10% Fetal Bovine Serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rh30 cells were crosslinked with formaldehyde, crosslinks were reversed, and samples were lysed according to GenPathway, Inc. FactorPath protocols.
|
| Label |
biotin
|
| Label protocol |
see GenPathway Inc. FactorPath protocol
|
| |
|
| Channel 2 |
| Source name |
input DNA from Rh30
|
| Organism |
Homo sapiens |
| Characteristics |
cells: Rh30 rhabdomyosarcoma cells
antibody: none
|
| Treatment protocol |
Rh30 cells were treated with vehicle or 40 nM rapamycin in serum-free media for 24 h.
|
| Growth protocol |
Cells were cultured in RPMI (Invitrogen) containing 10% Fetal Bovine Serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rh30 cells were crosslinked with formaldehyde, crosslinks were reversed, and samples were lysed according to GenPathway, Inc. FactorPath protocols.
|
| Label |
biotin
|
| Label protocol |
see GenPathway Inc. FactorPath protocol
|
| |
|
| |
| Hybridization protocol |
see GenPathway Inc. FactorPath protocol
|
| Scan protocol |
see GenPathway Inc. FactorPath protocol
|
| Description |
p73 Rh30 Rapamycin ChIP, array B
|
| Data processing |
The CEL files were analyzed using Affymetrix' Tiling Analysis Software. A two-sample analysis was performed to generate BAR files that contain the signal values for all probes on the arrays (moving statistic, ratio in linear scale ChIP/input). MaxGap = 400 bp, MinRun = 180 bp, intervals had signals >= 2.5.
Results file descriptions: The .bar files contain signals generated using Affymetrix' Tiling Analysis Software (moving statistic, ratio ChIP/input). The GSE15703_intervalbed.bed file contains p73 binding site intervals and peaks for the vehicle and rapamycin-treated samples. The BED file is available on the GSE15703 Series record.
|
| |
|
| Submission date |
Apr 16, 2009 |
| Last update date |
Jan 05, 2011 |
| Contact name |
Jennifer Pietenpol |
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Biochemistry
|
| Lab |
652 PRB
|
| Street address |
23rd Ave South at Pierce
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL4911 |
| Series (2) |
| GSE15704 |
ChIP-on-Chip data from Rh30 cells +/- rapamycin treatment |
| GSE15719 |
p73 activity and rapamycin treatment: ChIP-on-Chip and gene expression profiling studies |
|
