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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 04, 2021 |
| Title |
Cxxc1null-H3K4me3-rep2 |
| Sample type |
SRA |
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| Source name |
Cxxc1fl/fl;Gdf9-Cre mouse GV oocytes
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| Organism |
Mus musculus |
| Characteristics |
stain: C57BL/6
antibody: H3K4me3
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| Treatment protocol |
4 week mouse treated by PMSG 44 h
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| Growth protocol |
in vivo
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
STAR ChIP-seq was performed according to a protocol described previously (Zhang et al., 2016). Briefly, samples were directly lysed and fragmented by micrococcal nuclease (MNase) at 37 °C for 5 min before being incubated with the primary antibody overnight with rotation at 4 °C. The next day, 100 μg Dynabeads Protein A (Thermo Fisher Scientific) was added to each sample and incubated for 2–3 h with rotation at 4 °C. The beads were washed five times with 150 μl radioimmunoprecipitation assay buffer (RIPA) and once with 150 μl lithium chloride buffer. For each sample, beads were resuspended with 27 μl deionized H2O and 1 μl 10× Ex-Taq buffer (Takara, RR006B); 1 μl proteinase K (catalog no. 10910000; Roche) was added to each sample and incubated at 55 °C for 90 min to elute DNA from the beads. After incubation at 80 °C for 40 min to inactivate the proteinase K, the sample was subjected to TELP (tailing, extension, ligation and PCR) library preparation without DNA purification.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq data analysis.ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters “--nomodel --nolambda --broad -B --SPMR -g mm” and signal tracks for each sample were generated with “wigToBigWig” from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
WGBS data analysis. Raw reads were trimmed using TrimGalore (v 0.4.4) with default parameters. Then the reads were mapped to converted mm9 reference using bismark (v0.19.0) with parameters “--bowtie2 --non_directional”. PCR duplicates were removed. The cytosine was distinguished as CpG, CHG and CHH and the methylation levels were calculated separately.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Oct 19, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Li Shen |
| E-mail(s) |
shenlab@zju.edu.cn
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| Phone |
86-0571-88981751
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| Organization name |
Life Sciences Institute, Zhejiang University
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| Lab |
Shenlab
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| Street address |
866 Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE159581 |
Role of CxxC-finger Protein 1 in the Establishment of Epigenetic Landscapes in Mouse Oocytes |
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| Relations |
| BioSample |
SAMN16475157 |
| SRA |
SRX9302841 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4832685_GV-4w-Cfp1-Gdf9-KO-H3K4me3-rep2.unique_treat_pileup.bw |
103.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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