|
| Status |
Public on Dec 03, 2017 |
| Title |
AML12_shCtrl_rep2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
AML12
|
| Organism |
Mus musculus |
| Characteristics |
tissue: AML12 cells
condition: shCtrl
lenti-virus expression: Dam-LAMINB1
|
| Treatment protocol |
The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
|
| Growth protocol |
AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2X1e6 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 |
tissue: AML12 cells
condition: shCtrl
lenti-virus expression: Dam-only
|
| Treatment protocol |
The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
|
| Growth protocol |
AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2X1e6 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 |
Biological 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 100k bps. The smoothing procedure takes into consideration of the spatial correlation of signals.
|
| |
|
| Submission date |
Feb 21, 2017 |
| Last update date |
Feb 23, 2018 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Biomedical Sciences
|
| Street address |
130 DongAn Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL10448 |
| Series (2) |
| GSE95115 |
Genome-wide maps of nuclear lamina interactions in AML12 cells upon HNRNPU KD [DamID] |
| GSE95116 |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture |
|
