|
| Status |
Public on Nov 04, 2016 |
| Title |
NPC H3K27me3_R1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K27me3 ChIP DNA from 46c NPC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 46c NPCs N2B27 differentiation
chip antibody: H3K27me3 (Millipore 07-449)
|
| Growth protocol |
ESCs were cultured in GMEM+ Supplement, transfected using Lipofectamine 2000 reagents or differentiated in NPC using N2B27 protocol
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from 3x10e6 mESCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012) Antibody used for ChIP was H3K27me3 (Millipore 07-449).
|
| Label |
Cy3
|
| Label protocol |
one microgram genomic DNA was prepared and amplified using the Agilent Sample preparation protocol. All the amplified material was labelled with Cy3 or Cy5 by random priming using SureTag DNA Labelling kit according to the Agilent ChIP-chip protocol
|
| |
|
| Channel 2 |
| Source name |
Input DNA from 46c NPCs
|
| Organism |
Mus musculus |
| Characteristics |
tag: 46c NPCs N2B27 differentiation
chip antibody: none
|
| Growth protocol |
ESCs were cultured in GMEM+ Supplement, transfected using Lipofectamine 2000 reagents or differentiated in NPC using N2B27 protocol
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from 3x10e6 mESCs were prepared and resuspended in NB-R (85 mM NaCl, 5.5% Sucrose, 10mM TrisHCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2, 0.2 mM PMSF, 1 mM DTT), Micrococcal nuclease (MNase) digestion and native ChIP were performed as previously described (Eskeland et al. 2010, Pradeepa et al.2012) Antibody used for ChIP was H3K27me3 (Millipore 07-449).
|
| Label |
Cy5
|
| Label protocol |
one microgram genomic DNA was prepared and amplified using the Agilent Sample preparation protocol. All the amplified material was labelled with Cy3 or Cy5 by random priming using SureTag DNA Labelling kit according to the Agilent ChIP-chip protocol
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized and washed according to manufacturer´s protocol. A custom 8x60K mouse tiling array (Agilent Technologies) containing 51,504 probes was used.
|
| Scan protocol |
Arrays were scanned on a NimbleGen MS 200 Microarray scanner (Roche) using 100% laser power and 2μm resolution and Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
H3K27me3 ChIP-chip
Supplementary files for combined samples (R1, R2) linked to Series record:
NPC H3K27me3 Combined.wig.bedgraph
normalizedlog2ratios_CombinedSamples.txt (column: NPC H3K27me3 Combined)
|
| Data processing |
Raw signal intensities were quantified from TIFF images using MS 200 Data Collection software. Microarray data were analyzed in R using the bioconductor packages Beadarray and Limma according to the Epigenesys NimbleGen ChIP-on-chip protocol 43
|
| |
|
| Submission date |
Nov 04, 2016 |
| Last update date |
Nov 04, 2016 |
| Contact name |
Nezha Suzanne Benabdallah |
| E-mail(s) |
nsbenabdallah@gmail.com
|
| Organization name |
German Cancer Research Center, DKFZ
|
| Department |
Functional and Structural Genomics
|
| Lab |
Soft-Tissue Sarcoma
|
| Street address |
Im Neuenheimer Feld 581 (TP4)
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22635 |
| Series (2) |
| GSE89550 |
A new model for long-range chromatin reorganization linked to enhancer activation [Agilent_ChIP] |
| GSE89557 |
A new model for long-range chromatin reorganization linked to enhancer activation |
|
