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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 12, 2024 |
| Title |
KO_HDAC3 |
| Sample type |
SRA |
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| Source name |
Testis
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| Organism |
Mus musculus |
| Characteristics |
tissue: Testis
time: postnatal day 21
strain: C57BL/6
genotype: Knockout
chip antibody: HDAC3 (Abcam, ab7030)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh testes were collected from wild-type and Nkapl KO mice at postnatal day 21, ground into powder in liquid N2, and crosslinked by 1% formaldehyde, followed by quenching with glycine solution. Chromatin was fragmented by sonication in ChIP SDS lysis buffer (50 mM Tris-HCl, pH=8; 10 mM EDTA, pH=8; 1% SDS) using the Covaris-S220 sonicator. Crosslinked chromatin was incubated with indicated antibodies in ChIP dilution buffer (50 mM HEPES, pH7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxycholate) with protease inhibitors overnight. Crosslinking was reversed overnight at 65°C, and DNA was extracted by using phenol/chloroform/isoamyl alcohol.
Precipitated DNA was amplified for deep-sequencing. For ChIP-seq, equal DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were aligned to the mouse reference genome mm10 with BOWTIE software (bowtie2 version 2.3.4.3), followed by the removal of those reads that with low mapping quality and duplicated through sample amplification or sequencing.
Peak calling was carried out by using MACS2 (version 2.1.2, with options'-mfold 5, 50-p 0.0001'), on ChIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0).
Assembly: mm10
Supplementary files format and content: bigWig files
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| Submission date |
May 12, 2023 |
| Last update date |
Dec 12, 2024 |
| Contact name |
Chen Xu |
| E-mail(s) |
xuchendhr@outlook.com
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| Phone |
15090769649
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| Organization name |
Nanjing Medical University
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| Street address |
101 Longmian Avenue, Jiangning District
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE232398 |
NKAPL binding sites in mouse testis and the genome-wide occupancy of the SOX30/HDAC3 protein complex and RNA Pol II in the absence of NKAPL |
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| Relations |
| BioSample |
SAMN35061924 |
| SRA |
SRX20310036 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7329940_21C059_21d_KO_HDAC3.bw |
502.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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