|
| Status |
Public on Feb 14, 2012 |
| Title |
LMNB intensity averaged duplicates |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
2 LMNB-DAM and 2 Dam transduced 3T3 lines
|
| Organism |
Mus musculus |
| Characteristics |
inm protein: LMNB
|
| Treatment protocol |
Transduced with self-inactivating retroviruses bearing either a fusion-DAM (test) or Dam-alone (control)
|
| Growth protocol |
Standard 3T3 fibroblast. 10% FCS, DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As per Vogel et al 2008 (PMID:17545983)
|
| Label |
Cy5
|
| Label protocol |
Standard Affymetrix
|
| |
|
| Channel 2 |
| Source name |
Dam alone Chips are control
|
| Organism |
Mus musculus |
| Characteristics |
control: Control Dam Only construct
|
| Treatment protocol |
Transduced with self-inactivating retroviruses bearing either a fusion-DAM (test) or Dam-alone (control)
|
| Growth protocol |
Standard 3T3 fibroblast. 10% FCS, DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As per Vogel et al 2008 (PMID:17545983)
|
| Label |
Cy5
|
| Label protocol |
Standard Affymetrix
|
| |
|
| |
| Hybridization protocol |
Standard Affymetrix (10ug of DNA) for more details contact the University of Chicago Functional Genomics facility
|
| Scan protocol |
Standard Affymetrix
|
| Description |
As opposed to prior arrays which used 2 color hybs, these were done in a single color on separate chips
|
| Data processing |
Quantile normalized using Affymetrix tiling array software
REMEMBER TO USE THE 2006 GENOME BUILDS. THESE HAVE NOT BEEN LIFTED OVER (unless an updated probe library becomes available from Affy). We performed Dam-ID with LMNA, included in this file are probe positions and intensities (can be displayed in IGB using the 2006 genome build) and are in the process of recovering the .Cel files from a failed hard drive, when available they will be added to the submission. If you would like the .bar files (more useful anyway, contact Joseph Zullo. GADAcallsMerged is the annotation of the LADs as called by the GADA algorithm.
Both Samples in this Series use the same 2 control CEL files available on the Series record (Dam 0519.CEL and Dam 0612.CEL)
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Feb 14, 2012 |
| Contact name |
Joseph M Zullo |
| E-mail(s) |
joseph_zullo@hms.harvard.edu, jmz4@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
MGCB
|
| Lab |
Singh
|
| Street address |
929 E 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL6448 |
| Series (2) |
| GSE35777 |
A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array] |
| GSE36049 |
A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina |
|
