|
| Status |
Public on Nov 10, 2011 |
| Title |
Control No Treat H3K9Ac |
| Sample type |
SRA |
| |
|
| Source name |
Control No Treat H3K9Ac
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone Marrow
cell-type: Macrophage
mutation: HDAC3 floxed
treatment: BSA
chip antibody: H3K9Ac (Upstate Biotechnologies, 06-942)
|
| Treatment protocol |
Macrophages were treated with either control vehicle, 0.1% bovine serum albumin (BSA) or 10ng/mL of IL-4 for 24 hours.
|
| Growth protocol |
Bone marrow derived macrophages were obtained by culturing bone marrow from 12-16 week old male C57Bl/6J mice in 30% L929 conditioned medium for six days, changing the media on the fourth day of culture. Cells were replated on day 6, allowed to rest overnight and then treated accordingly. Control macrophages were from mice with exons 4-7 of HDAC3 floxed with loxP sites (HDAC3 floxed). HDAC3 KO macrophages were from mice expressing Cre recombinase under the control of the lysozyme M promoter and with floxed HDAC3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% PFA for 15 minutes and quenched with glycine. Nuclei were harvested and lysed. Extracts were sonicated using a Bioruptor (Diagenode). Immunoprecipiation using anti-HDAC3 (Abcam, ab7030) and anti-H3K9Ac (Upstate Biotechnologies, 06-942) were performed and resulting chromatin was isolated. Control Input DNA for comparison with the H3K9Ac ChIP was generated by pooling equal amounts of nuclear extract from Control and HDAC3 KO macrophages with and without IL-4 treatment prior to immunoprecipitation. ChIP and Input DNA was prepared from bone marrow derived macrophages for sequencing according to the amplification protocol from Illumina. DNA for the HDAC3 ChIP-seq was obtained by pooling DNA from two independent ChIPs each using a pool of four mice for each condition while the DNA for the H3K9Ac ChIP-seq was obtained from a pool of four mice for each condition.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 3
|
| Data processing |
Sequencing was performed by the Functional Genomics Core at the University of Pennsylvania. Sequence reads of 36 bp were obtained using the Solexa Analysis Pipeline, and were mapped to the mouse genome (mm8). All but one of the identically aligning reads were removed to minimize PCR bias. Regions that overlapped with peaks in the input data were discarded.
|
| |
|
| Submission date |
Nov 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Logan J Everett |
| Organization name |
U.S. Environmental Protection Agency
|
| Department |
Office of Research and Development
|
| Lab |
Center for Computational Toxicology and Exposure
|
| Street address |
109 T.W. Alexander Dr
|
| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE33596 |
Histone Deacetylase 3 is an Epigenomic Brake in Macrophage Alternative Activation (ChIP-Seq) |
| GSE33609 |
Histone Deacetylase 3 is an Epigenomic Brake in Macropahge Alternative Activation |
|
| Relations |
| SRA |
SRX105111 |
| BioSample |
SAMN00750793 |
| Named Annotation |
GSM830473_mlsm_140_3_rd.bed.gz |
