|
| Status |
Public on Feb 09, 2017 |
| Title |
H3K27ac 195minLPS+IL-10-c10 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow Derived Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
genotype: IL10-/-RAG2-/-
strain: 129S6/SvEvTac
cell type: Bone Marrow Derived Macrophage
antibody: H3K27ac (Abcam ab4729)
|
| Treatment protocol |
Untreated, LPS (1 ng/mL) for 195 min, LPS and IL-10 (1 ng/mL) for 195 min (c10), LPS for 195 min and IL-10 for the last 30 min of the stimulation (a10)
|
| Growth protocol |
Bone marrow precursors were grown in M-CSF conditioned media containing FBS for 5 days prior to stimulation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Macrophages were plated at 2 x 107 cells per condition and after stimulation fixed for 10 minutes in 1% formaldehyde. Chromatin was isolated and sheared by sonication (10 cycles, 20 s on, 30 s rest). After aliquoting an input fraction, 4 x 10^6 cells were incubated overnight at 4°C with Protein A Dynabeads pre-coupled with 5 µg of anti-H3K27ac Ab (Abcam, ab4729). After incubation, the beads were washed sequentially with a low salt buffer, high salt buffer, lithium chloride buffer, and TE buffer. DNA-protein complexes were eluted from the beads with 1% SDS TE buffer at 65°C for 15 min. Input and IP crosslinks were reversed by overnight incubation at 65°C. DNA was treated with proteinase K and RNase A before purification with the QIAquick PCR Purification kit.
using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
195min LPS +c10
|
| Data processing |
Trim_galore
Bowtie2
MACS2
DiffBind
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited txt of normalized peak values
|
| |
|
| Submission date |
Aug 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bruce Horwitz |
| E-mail(s) |
bhorwitz@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Pathology
|
| Street address |
77 Ave Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE86168 |
Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation [h3k27 ChIP] |
| GSE86170 |
Inhibition of inflammatory gene transcription by IL-10 is associated with rapid suppression of LPS-induced enhancer activation |
|
| Relations |
| BioSample |
SAMN05713638 |
| SRA |
SRX2060963 |
