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| Status |
Public on Jan 22, 2017 |
| Title |
WT_ATAC-seq_fibroblast_rep_1 |
| Sample type |
SRA |
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| Source name |
Ear
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype: Aire+/+
cell type: fibroblasts
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as MECs and CD45-EpCAM-CD31-Ter-119-Sca-1+ as earskin fibroblasts
Cells were suspended in 100ul of cold hypotonic lysis buffer [10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550g for 30 min. The pellet was re-suspended in 5ul of transposition reaction mix [1ul of Tagment DNA Enzyme and 2.5uL of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5ul H2O], and was incubated for 60 min at 37°C for DNA to be fragmented and tagged. For library preparation, two sequential 7-cycles of PCR were performed in order to enrich small tagmented DNA fragments. After the first PCR, the libraries were selected for small fragments (less than 600bp) using SPRI beads followed by a second round of PCR with the same conditions in order to obtain the final library
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Short reads (50bp, forward; 34bp, reverse) were aligned to the mouse reference genome (mm10) using bowtie aligner version 2.2.4
Reads with multiple alignments were removed with samtools (v1.1) and de-duplicated with picard (v1.130)
Reads mapping to mitochondrial DNA were removed before analysis.
To identify peaks from ATAC-seq reads, we used the HOMER package makeTagDirectory followed by the findPeaks command with the ‘factor’ parameter.
To visualize individual ATAC-seq data on Integrative Genomics Viewer (IGV), we converted bam output files into normalized bigwig format using the bamCoverage function in deepTools (v1.6) with options – fragmentLength 200 –normalizeUsingRPKM
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Dec 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
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| Phone |
617-432-7747
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| Organization name |
Harvard Medical School
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| Department |
Microbiology and Immunobiology
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| Lab |
CBDM
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE92594 |
Aire, guardian of immunological tolerance, binds to and activates super-enhancers [ATAC-seq] |
| GSE92654 |
Aire, guardian of immunological tolerance, binds to and activates super-enhancers |
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| Relations |
| BioSample |
SAMN06166403 |
| SRA |
SRX2436322 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2433164_WT_Fibroblast_1.without.adapter.mapped_1align.woChrM.sorted.uniq.RPKM.bigwig |
76.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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