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Sample GSM1546000 Query DataSets for GSM1546000
Status Public on Dec 05, 2014
Title Spleen_K4Me1_rep1
Sample type SRA
 
Source name Spleen red pulp macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: Spleen red pulp macrophages
chip antibody: anti-H3K4me1
chip antibody vendor/cat.#: Abcam ab8895 and Millipore 07-436 mixed ratio 1:1
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
E-mail(s) ido.amit@weizmann.ac.il
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
Relations
BioSample SAMN03196811
SRA SRX760585
Named Annotation GSM1546000_merged_Spleen_K4Me1_1.bigWig

Supplementary file Size Download File type/resource
GSM1546000_merged_Spleen_K4Me1_1.bigWig 120.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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