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Sample GSM1545944 Query DataSets for GSM1545944
Status Public on Dec 05, 2014
Title MA_i7_ATAC_Spleen1
Sample type SRA
 
Source name Spleen red pulp macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: Spleen red pulp macrophages
Extracted molecule genomic DNA
Extraction protocol Cells were sorted into MACS buffer, washed and lysed in 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% or 0.5% Igepal CA-630. Nuclei were pelleted by centrifugation for 30min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol (some samples used read2 to read molecule barcodes only)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing HISEQ split using cassava Y60,I10
alignment using bowtie 1.0.0. command (bowtie -a -m 1 --sam --best --strata -v 2 mm9)
makeTagDirectory -tbp
makeUCSCfile -bigWig -fsize 1e20
Genome_build: mm9
 
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)
GSE63338 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ATAC-seq]
GSE63341 Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment
Relations
BioSample SAMN03196831
SRA SRX760529
Named Annotation GSM1545944_MA_i7_ATAC_Spleen1.bigWig

Supplementary file Size Download File type/resource
GSM1545944_MA_i7_ATAC_Spleen1.bigWig 76.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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