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| Status |
Public on Apr 30, 2019 |
| Title |
MEL_DNase_D5R1 |
| Sample type |
SRA |
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| Source name |
MEL
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| Organism |
Mus musculus |
| Characteristics |
cell type: MEL
time: D5
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| Treatment protocol |
MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result.
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| Growth protocol |
Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA). Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Biological replicates of DNase-seq libraries for uninduced and induced MELs were built as previously described except for the DNA purification below (Hesselberth et al. 2009). Briefly, 20 million nuclei were digested with 80U/ml DNaseI (Catalog number D4527, Sigma-Aldrich, St.Louis, MO) for 3 minutes at 37 degree Celsius. Following 1-hour digestion with proteinase K (Sigma-Aldrich), DNA samples were purified by phenol/chloroform (Fisher Scientific, Waltham, MA) and precipitated by isopropanol (Fisher Scientific) and sodium acetate, pH 5.5 (Life Technologies). DNA fragments between 25 and 100bp were purified by gel electrophoresis and constructed into sequencing libraries.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
DNAse-Seq
processed_data_file: MEL_D5R1_DHS.bed, MEL_D5_R1R2_intersected_DHS.bed, MEL_D5_DNase_footprints_p_minus20.bed, MEL_D0D5_consolidated_DHS.bed, MEL_3kb_vertices.bed, MEL_1kb_vertices.bed
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| Data processing |
Reads were trimmed to 36bp and paired-end mapped to the mm9 reference genome using bowtie using parameters -S -q -v 2 -k 1 -m 1 -X 1000.
DNaseI hypersensitive sites were identified using the hotspot algorithm for each sample. DNaseI hotspot calls that passed the 1% FDR cutoff were used for further downstream analysis.
The intersection between hotspot calls of biological replicates is required to reciprocally overlap by 70% using Bedtools software
genome build: mm9
processed data files format and content: DNase-seq hotspot bed files from each individual samples, the intersected hotspot bed files from each differentiation stage and the consolidated hotspot bed file from both differentiation stages, together with Wellington footprint bed files with p-value lower than 10^(-20) from both undifferentiated and differentied MEL DNase-seq
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| Submission date |
May 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Marissa Macchietto |
| E-mail(s) |
mmacchie@umn.edu
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| Organization name |
University of Minnesota, Minneapolis
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| Department |
Minnesota Supercomputing Institute
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| Street address |
117 Pleasant Street SE
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| City |
Minneapolis |
| ZIP/Postal code |
55455 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE67955 |
The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation |
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| Relations |
| BioSample |
SAMN03580696 |
| SRA |
SRX1016129 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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