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Sample GSM2296669 Query DataSets for GSM2296669
Status Public on Feb 09, 2017
Title H3K27ac 195min LPS 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
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 SAMN05713641
SRA SRX2060960

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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