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| Status |
Public on Aug 08, 2016 |
| Title |
GA1843-mouse-9905-H4K16ac |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
strain: mix genetic background of 129/FVB/Black Swiss
genotype/variation: wild type
age: 3 months
antibody (vendor, batch/lot#, catalog#) or reference: anti-H4K16ac, Santa Cruz, sc-8662-R
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| Growth protocol |
Mice are maintained at a 12-h light environment. At the experiments time, mice were sacrificedbetween 9AM to 11AM by Avertin injection. Blood were drained. Fresh liver samples were snap frozen with liquid nitrogen.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The fresh liver samples were snap frozen with liquid nitrogen, then powdered by Bessman Tissue Pulverizer. Chromatins were extracted from the hepatic powder based on previous publication (Cell. 2007 May 18;129(4):823-37.)
Library constructions for ChIP-Seq follow the protocol as described previously in (Cell. 2007 May 18;129(4):823-37. PMID: 17512414).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Chromatin IP against H4K16ac
GA1843_mouse_9905_H4K16ac_noDup-W200-G400-islands-summary-FDR0.001.txt.gz
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| Data processing |
Basecalls performed using GAPipeline 1.3.2
Sequence reads were obtained and mapped to the mouse (mm8) genomes with bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained.
ChIP-Seq read enriched regions were called by using SICER v 1.03 (window size = 200, gap size = 400, FDR = 0.001) (PMID: PMC2732366)
Genome_build: mm8
Supplementary_files_format_and_content: The seven-column files are outputs from SICER. From left to right the columns are for:
chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold
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| Submission date |
Jan 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
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| Organization name |
West Virginia University
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| Department |
MicroBiology, Immunology, and Cell Biology
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| Lab |
2072A, HSC North, Floor 2
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| Street address |
64 Medical Center Drive
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| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE54449 |
Negative reciprocal regulation between SIRT1 and Per2 in circadian clock during aging (ChIP-Seq) |
| GSE54451 |
Negative reciprocal regulation between SIRT1 and Per2 in circadian clock during aging |
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| Relations |
| BioSample |
SAMN02597921 |
| SRA |
SRX451271 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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