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Status |
Public on Dec 05, 2014 |
Title |
MA_g12_ATAC_Mono1 |
Sample type |
SRA |
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Source name |
Monocytes
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: Bone marrow cell type: Monocytes
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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)
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 1500 |
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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
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Submission date |
Nov 17, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Ido Amit |
E-mail(s) |
ido.amit@weizmann.ac.il
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Phone |
972-8-9343338
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Organization name |
Weizmann Institute of Science
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Department |
Immunology
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Street address |
234 Herzl st.
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City |
Rehovot |
ZIP/Postal code |
760001 |
Country |
Israel |
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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 |
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Relations |
BioSample |
SAMN03196836 |
SRA |
SRX760538 |
Named Annotation |
GSM1545953_MA_g12_ATAC_Mono1.bigWig |
Supplementary file |
Size |
Download |
File type/resource |
GSM1545953_MA_g12_ATAC_Mono1.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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