|
| Status |
Public on Dec 05, 2014 |
| Title |
MA_i4_ATAC_LI1 |
| Sample type |
SRA |
| |
|
| Source name |
Large intestine macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Large intestine
cell type: Large intestine 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 |
SAMN03196840 |
| SRA |
SRX760541 |
| Named Annotation |
GSM1545956_MA_i4_ATAC_LI1.bigWig |
