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| Status |
Public on Oct 20, 2023 |
| Title |
pahari_F_H3K4me3 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus pahari |
| Characteristics |
tissue: Liver
seq_assay: ChIP
common_name: Shrewlike Mouse
Sex: F
chip antibody: H3K4me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
pahari-H3K4me3.bigwig
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| Data processing |
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed
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| Submission date |
May 11, 2022 |
| Last update date |
Oct 20, 2023 |
| Contact name |
Mariam Okhovat |
| Organization name |
Oregon Health and Science University
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| Department |
Medicine
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| Street address |
3030 S Moody Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL32023 |
| Series (1) |
| GSE197926 |
TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function |
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| Relations |
| BioSample |
SAMN28196660 |
| SRA |
SRX15239157 |
| 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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