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| Status |
Public on Feb 04, 2021 |
| Title |
Cerebellum wild type rep4 |
| Sample type |
SRA |
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| Source name |
cerebellum
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 9 weeks
genotype: wild type
tissue: cerebellum
chip antibody: Anti-acetyl-Histone H3 (Lys9), Millipore 07-352
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was fixed in 1% formaldehyde for 10 min at room temperature and quenched with 111 μl 1.25M glycine. Tissue was homogenized in nuclei isolation buffer (50mM Tris-HCl pH8, 60mM KCl, 0.5% NP-40), lysed in lysis buffer buffer (50mM Tris-HCl pH8, 10mM EDTA pH8, 0.5mM EGTA pH8, 0.5% SDS) and sonicated on a Pico Biorupter for three 8x cycles of 30 sec on, 90 sec off at 4°C Chromatin was then diluted in dilution buffer (20mM Tris-HCl pH8, 2mM EDTA pH8, 150mM NaCl, 1% Triton X100). After incubation with anti-H3K9ac coated magnetic beads, DNA waswashed, treated with RNAse and proteinase K and cleaned up with g the Zymo ChIP DNA clean and concentrator kit (Zymo #D5201) following the manufacturer’s protocol.
Library was prepared using standard UCSD Genomics core protocols to generate single ended TruSeq adapters. Library PCR amplification was performed at 15 cycles and agarose gel size selection performed at the 300-600 bp range. Samples were analyzed by Agilent Tapestation to determine concentrations and loaded into the IGM Core’s Illumina HiSeq 4000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Model-based Analysis of ChIP-Seq (MACS) algorithm used to call peaks:
The paired Input and ChIP FASTQ files were input to FASTQ Groomer, FASTQ Quality Trimmer (quality score >30)
Reads were mapped to mm10 using Bowtie2
Aligned reads were filtered for duplicates by RmDup
MACS was then run with these paired files using an MFOLD high confidence threshold of 16, an estimate band size of 300 bp, and a peak cutoff threshold of P <1e-05
Genome_build: mm10
Supplementary_files_format_and_content: Peak BED files
Supplementary_files_format_and_content: The bigWig format to display data in the Genome Browser as a graph
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| Submission date |
Feb 03, 2021 |
| Last update date |
Feb 05, 2021 |
| Contact name |
Pawel Michal Switonski |
| Organization name |
University of California, Irvine
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| Department |
Department of Pathology & Laboratory Medicine
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| Lab |
La Spada
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| Street address |
1001 Health Sciences Road
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| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE166118 |
Epigenetic Dysregulation by Polyglutamine-expanded Ataxin-7 In The mouse model of SCA7 |
| GSE166123 |
Epigenetic dysregulation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7 |
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| Relations |
| BioSample |
SAMN17771890 |
| SRA |
SRX10015172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5061960_Cb_WT4_H3K9ac.bed.gz |
22.3 Kb |
(ftp)(http) |
BED |
| GSM5061960_Cb_WT4_H3K9ac.bigwig |
131.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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