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| Status |
Public on Dec 05, 2014 |
| Title |
MA_g05_ATAC_Lung1 |
| Sample type |
SRA |
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| Source name |
Lung macrophages
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lung
cell type: Lung macrophages
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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 |
SAMN03196837 |
| SRA |
SRX760530 |
| Named Annotation |
GSM1545945_MA_g05_ATAC_Lung1.bigWig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1545945_MA_g05_ATAC_Lung1.bigWig |
37.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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