|
| Status |
Public on May 07, 2008 |
| Title |
Tig3 human fibroblast cells, Emerin DamID, platform chr4 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tig3 Human fibroblast cells, expressing Emerin-Dam
|
| Organism |
Homo sapiens |
| Characteristics |
Emerin-Dam (EXPERIMENTAL)
|
| Treatment protocol |
Tig3 cells are transducted with the lentiviruses. gDNA is harvested after 3 days incubation
|
| Growth protocol |
see Nat Protoc. 2007;2(6):1467-78. for detailed growth, treatment, and extraction protocols. In short: lentivirus is transfected in, and harvested from 293Tcells, grown in DMEM + 10% FCS + Pen/Strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA is isolated using the Dneasy Tissuekit
|
| Label |
Cy5,Cy3
|
| Label protocol |
Samples were labeled by NimbleGen Systems, Reykjavik, Iceland
|
| |
|
| Channel 2 |
| Source name |
Tig3 Human fibroblast cells, expressing Dam
|
| Organism |
Homo sapiens |
| Characteristics |
Dam (REFERENCE)
|
| Treatment protocol |
Tig3 cells are transducted with the lentiviruses. gDNA is harvested after 3 days incubation
|
| Growth protocol |
see Nat Protoc. 2007;2(6):1467-78. for detailed growth, treatment, and extraction protocols. In short: lentivirus is transfected in, and harvested from 293Tcells, grown in DMEM + 10% FCS + Pen/Strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA is isolated using the Dneasy Tissuekit
|
| Label |
Cy3,Cy5
|
| Label protocol |
Samples were labeled by NimbleGen Systems, Reykjavik, Iceland
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized by NimbleGen Systems, Reykjavik, Iceland
|
| Scan protocol |
Arrays were scanned by NimbleGen Systems, Reykjavik, Iceland
|
| Description |
na
|
| Data processing |
The log2-ratio of Dam-Fusion signal over Dam-only signal was calculated. Subsequently, normalization was applied within arrays using loess. All 16 arrays were median and variance normalized on the basis of the common 9731 probes on all 16 arrays. Replicate samples in reverse dye orientation were averaged. Finally, the median over the entire array set was subtracted from the data. 8 data files are included which give the final normalized values (GPLxxx_norm_value.tsv)
|
| |
|
| Submission date |
Aug 22, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Bas van Steensel |
| E-mail(s) |
b.v.steensel@nki.nl
|
| Phone |
+ 31 20 512 2040
|
| Fax |
+31 20 669 1383
|
| URL |
http://www.nki.nl/nkidep/vansteensel
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
division of Molecular Biology
|
| Lab |
van Steensel group
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL5729 |
| Series (2) |
| GSE8854 |
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions |
| GSE51334 |
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions |
|
