|
| Status |
Public on Apr 30, 2013 |
| Title |
Polyploid (16C-128C) MKs_aCGH_Replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
C57Bl/6J bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell population: Polyploid MKs
|
| Treatment protocol |
MKs were treated with 25ng/ml human thrombopoietin for 4 days to induce differentiation and polyploidization.
|
| Growth protocol |
Bone marrow cells from twenty-four 6-8-week old C57B6/J mice were culture with IMDM media (Invitrogen) containing 10% fetal bovine serum, 1% penicillin-streptomycin, 4mM L-glutamine, and 25ng/ml human thrombopoietin for 4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Polyploid and diploid MKs were lysed in CHIP buffer (50mM HEPES pH. 7.5; 140mM NaCl; 1mM EDTA; 1% Triton-X100; 0.1% Na deoxycholate), sonicated, and treated with proteinase K and RNAse. DNA was isolated following standard phenol:chloroform extraction.
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.
|
| |
|
| Channel 2 |
| Source name |
C57Bl/6J bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: Diploid MKs
|
| Treatment protocol |
MKs were treated with 25ng/ml human thrombopoietin for 4 days to induce differentiation and polyploidization.
|
| Growth protocol |
Bone marrow cells from twenty-four 6-8-week old C57B6/J mice were culture with IMDM media (Invitrogen) containing 10% fetal bovine serum, 1% penicillin-streptomycin, 4mM L-glutamine, and 25ng/ml human thrombopoietin for 4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Polyploid and diploid MKs were lysed in CHIP buffer (50mM HEPES pH. 7.5; 140mM NaCl; 1mM EDTA; 1% Triton-X100; 0.1% Na deoxycholate), sonicated, and treated with proteinase K and RNAse. DNA was isolated following standard phenol:chloroform extraction.
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.
|
| |
|
| |
| Hybridization protocol |
Samples were co-hybridized to a 1-million probe custom tiling array designed for C57BL/6J (Agilent-027414).
|
| Scan protocol |
Slides were washed and scanned using an Agilent microarray scanner.
|
| Description |
Replicate 1: bone marrow cells were differentiated into MKs after culturing with thrombopoietin for 4 days.
|
| Data processing |
Using the Ringo package in R, probes were median-normalized and smoothened by running medians prior to calling under-replicated or amplified regions, defined by at least 5 adjacent probes with a fold change (copy number vs. overall ploidy) greater than 1.3. Microarrays were also converted into Nimblegen format and processed by MA2C software.
|
| |
|
| Submission date |
Apr 04, 2013 |
| Last update date |
Apr 30, 2013 |
| Contact name |
Jessica Von Stetina |
| E-mail(s) |
vstetina@wi.mit.edu
|
| Organization name |
Whitehead Institute
|
| Lab |
Orr-Weaver
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL10448 |
| Series (2) |
| GSE45778 |
Murine polyploid trophoblast giant cells (TGCs) from day E9.5 implantation sites (experimental) vs E9.5 diploid embryos (control) |
| GSE45787 |
Murine polyploid trophoblast giant cells from day E9.5 implantation sites |
|
