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| Status |
Public on Oct 19, 2022 |
| Title |
Pcgf1_f/f_H3K27me3_2 |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: B6CBAF1/J
cell type: Hemtopoietic progenitor cells (IdHPs)
passage: 15-18
genotype: Pcgf1 fl/fl
antibody: H3K27me3 (Merk Millipore, 07-449)
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| Growth protocol |
Culture with TSt4 stroma cells by IMDM supplemented with IL7, SCF,Fl3L
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP for FLAG, RING1B, SUZ12, H3K27me3 and H3K27ac were performed as described previously (Isono et al., 2013). Cultured IdHP cells were cross-linked with 1% formaldehyde/PBS for 10 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with indicated antibodies. ChIP for H2AK119ub was performed as described before (Mochizuki-Kashio et al., 2015). Cultured IdHP cells were cross-linked with 0.5% formaldehyde/PBS for 2 min at 37℃. Chromatin was sheared and used for each immunoprecipitation.
ChIP products and fragmented DNAs fragmentd by MNase were subjected to library preparation by NEBNext UltraⅡ DNA library preparation kit for Illumina(E7645; New England Biolabs).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Pcgf1_f/f_H3K27me3_2
peak file = H3K27me3_Peaks.txt
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| Data processing |
For ChIP-seq without spike-in genome, reads were aligned to mm9 using bowtie2(Langmead et al., 2012). ChIP-seq experiments which contained a spike-in genome were aligned against concatenated genome of mm9 and dm3 using bowtie2 and resulting SAM files were then split such that reads aligning to mouse and drosophilia were placed in separate files. The SAM files were converted to the BAM format using Samtools, version 1.6.0 (Li et al., 2009). The PCR duplicates were removed by Picardtools (http://broadinstitute.Github.io/picard).
he BAM files were converted to bigwig files by deepTools2 (Ramirez et al. 2016) for visualization. For comparison across ChIP-seq samples without spike-in genome, the bigwig files were normalized to reads per million mapped sequence reads (RPKM). For ChIP-seq with spike-in genome, RPKM were further normalized according to normalization factors calculated as 1 over the number of reads (per million) mapping to drosophilia as previously reported(Orland et al., 2016).
Genome_build: mm9 or concateenated genomes of Mm9 and dm3
Supplementary_files_format_and_content: bigwig files described in the data processing step columns
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| Submission date |
Dec 06, 2019 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Junichiro Takano |
| E-mail(s) |
junichiro.takano@riken.jp
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| Organization name |
RIKEN
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| Department |
IMS
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| Lab |
Developmental Genetics
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| Street address |
Tsurumi-ku-Suehirocho-1-7-22
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| City |
Yokohama-shi |
| State/province |
Kanagawa-kwn |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (2) |
| GSE141559 |
Gene regulation by PCGF1 in hematopoietic progenitor cells [ChIP, MNaseSeq] |
| GSE141560 |
Hematopoietic progenitor cells |
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| Relations |
| BioSample |
SAMN13496743 |
| SRA |
SRX7278141 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4206963_S09946.bw |
59.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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