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Sample GSM1545975 Query DataSets for GSM1545975
Status Public on Dec 05, 2014
Title SI_K27Ac_rep1
Sample type SRA
Source name Small intestine macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Small intestine
cell type: Small intestine macrophages
chip antibody: anti-H3K27ac
chip antibody vendor: Abcam
chip antibody cat. #: ab4729
Extracted molecule genomic DNA
Extraction protocol Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
Data processing Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
Submission date Nov 17, 2014
Last update date May 15, 2019
Contact name Ido Amit
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
Platform ID GPL18480
Series (2)
GSE63339 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ChIP-seq]
GSE63341 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment
BioSample SAMN03196843
SRA SRX760560
Named Annotation GSM1545975_merged_SI_K27Ac_1.bigWig

Supplementary file Size Download File type/resource
GSM1545975_merged_SI_K27Ac_1.bigWig 110.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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