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| Status |
Public on Aug 10, 2016 |
| Title |
GFP Input ChIP-Seq |
| Sample type |
SRA |
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| Source name |
Input DNA for GFP sample
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
cell type: Chondrocytes
genotype/variation: wild-type
transduction: GFP control adenovirus
chip antibody: None
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to NuGene Ultralow library prep kit V2
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
GFP control adenovirus
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| Data processing |
bcl2fastq v1.8.4 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: mm10
Supplementary_files_format_and_content: This file contains a list of peaks, from left to right are: chr, start, end, peak ID, integer score for display, fold-change, -log10pvalue, -log10qvalue and peak summit position relative to peak start
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| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Jane Westendorf |
| E-mail(s) |
Westendorf.Jennifer@mayo.edu
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| Organization name |
Mayo Clinic
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| Street address |
200 First Street SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE75547 |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq] |
| GSE75552 |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes |
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| Relations |
| BioSample |
SAMN04304507 |
| SRA |
SRX1457514 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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