|
| Status |
Public on Dec 01, 2019 |
| Title |
DamID AML12_shCtrl_rep2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
AML12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AML12 cells
lenti-virus expression: Dam-LAMINB1
|
| Treatment protocol |
The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.
|
| Growth protocol |
AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2×106 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.
|
| |
|
| Channel 2 |
| Source name |
AML12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AML12 cells
lenti-virus expression: Dam-only
|
| Treatment protocol |
The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then AML12 cells were infected with 200 μl of virus concentrate in a well of six-well-plates. Medium was changed 24 hours after transfection, and then collect cells 5 days after transfection.
|
| Growth protocol |
AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2×106 AML12 cells were planted in 6-well plates, and infected with lenti-virus expressing Dam or Dam-Lamin B1 after 48 hours. gDNA was isolated with the Dneasy Tissue kit (Qiagen) per the manufacturers protocol after 72 hours. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR),see Vogel et al., 2008, Nature Protocols for details.
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA samples were differentially labeled with Invitrogen’s BioPrime Total for Agilent aCGH labeling kit.
|
| |
|
| |
| Hybridization protocol |
Hybridized to Agilent-027414 arrays.
|
| Scan protocol |
Scanned on an Agilent Technologies Scanner G2505C.
|
| Description |
Replicate 2 of 2 shCtrl AML12 cells
|
| Data processing |
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization. we also smoothed the probe signals using a moving average approach with a window size of 40k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.
|
| |
|
| Submission date |
Nov 27, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Street address |
130 Dongan Rd.
|
| City |
ShangHai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL10448 |
| Series (2) |
| GSE125037 |
The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation |
| GSE141109 |
Genome-wide maps of nuclear lamina interactions in AML12 cells upon Safb KD [DamID] |
|
