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Sample GSM2296673 Query DataSets for GSM2296673
Status Public on Feb 09, 2017
Title H3K27ac 195minLPS+IL-10-c10 Rep3
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 SAMN05713637
SRA SRX2060964

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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