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| Status |
Public on Sep 01, 2010 |
| Title |
Cells_CH12.LX_0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212 |
| Sample type |
genomic |
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| Source name |
Sample Type: Cells, Cell Type: CH12.LX
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| Organism |
Mus musculus |
| Characteristics |
array type: Mm35b_P07R
pooled from multiple samples: No
number of cells seeded: 1X10^5 cells/ml, 25ml in P150s
units of harvest time point: hr
antibody name: Aryl hydrocarbon receptor, pAb (affinity purified); Vendor: Biomol (Plymouth Meeting, PA); Catalog #: SA210-0100
sample type: ChIP
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| Biomaterial provider |
Nadira De Abrew, The Hamner Institutes for Health Sciences, 6 Davis Drive, Research Triangle Park, NC, 27709, Nadira De Abrew, ndeabrew@thehamner.org, 9195581388
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| Treatment protocol |
in vitro Treatment: DMSO, Units of Treatment Repeat: nM, Treatment Duration: 1, Units of Duration: hr, Vehicle for Chemical: DMSO, Route of Exposure: Media
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| Growth protocol |
Growth Media: RPMISAdvance, HIFBS, HEPES, Pen/Strepp, L Glutamine, Mercaptoethanol, Amount of Media: 25, Units of Media: ml
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction Method: Addition of lysis buffer followed by disruption with a Dounce homogenizer. Lysates sonicated and DNA sheared to an average length of 300-500bp
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| Label |
biotin
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| Label protocol |
standard Affymetrix protocol
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| Hybridization protocol |
standard Affymetrix procedures
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| Scan protocol |
standard Affymetrix procedures
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| Description |
0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212: CH12.LX cells were treated with either TCDD (10nM) or vehicle (0.01% DMSO) for 1 hr and cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a Nanodrop ND-1000 spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein - agarose beads. Factor-bound DNA sequences were isolated using antibodies against AhR. After incubation at 4°C overnight, protein-agarose beads were used to isolate the immune complexes. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Following purification ChIP DNA was labeled, fragmented and hybridized to Affymetrix GeneChip Mouse Tiling 2.0 Array Sets, hybridized arrays were then washed and scanned using a GeneChip Fluidics Station 450 and a GeneChip 3000 scanner.
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| Data processing |
Affymetrix GCOS 1.0
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| Submission date |
Aug 09, 2010 |
| Last update date |
Aug 19, 2010 |
| Contact name |
Russell Scott Thomas |
| E-mail(s) |
rthomas@thehamner.org
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| Phone |
919-558-1311
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| Fax |
919-558-1300
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| Organization name |
The Hamner Institutes for Health Sciences
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| Street address |
6 Davis Drive
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL6450 |
| Series (1) |
| GSE23708 |
Chromatin Immunoprecipitation Analysis of Aryl Hydrocarbon Receptor Binding in a Mouse B-cell Line (CH12.LX) Activated with Lipopolysaccharide and Treated with 2,3,7,8-Tetrachlorodibenzo-p-dioxin |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM575821_0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212.CEL.gz |
25.1 Mb |
(ftp)(http) |
CEL |
| GSM575821_0412HI_AhR_IP_DMSO1_Mouse_ArrayG_081212.bar.gz |
32.4 Mb |
(ftp)(http) |
BAR |
| Processed data provided as supplementary file |
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