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| Status |
Public on May 31, 2021 |
| Title |
H2AK119ub_ERT2-Cre_Pcgf1Control_ES_rep2 |
| Sample type |
SRA |
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| Source name |
ES
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| Organism |
Mus musculus |
| Characteristics |
tamoxifen treatment: without 4-OHT
genotype: ERT2-Cre;Pcgf1f/f
cell type: embryonic stem cell
antibody: H2AK119ub1(CST,8240S)
replicate: 2
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| Growth protocol |
Embryonic stem cells (ESCs) were cultured with LIF (1U: Laboratory made), SU5402 (Altair corporation), PD184352 (Altair corporation) and CHIR99021 (Altair corporation) on MEF. For Embryoid Body (EB) formation, ESCs were cultured without LIF, SU5402, PD184352, CHIR99021 for 2 days on low attach culture dish. For epiblast stem cell (EpiSC) establishment, Embryoid Body (day2) are dispersed. And the cells were cultured on MEF with ActivinA (Peprotech), bFGF (Wako) and IWP-2 (Wako) on MEF in F12 medium (Gibco) 1%KSR (Gibco).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&Tag was performed as described in Kaya-Okur et al., (Kaya-Okur et al., 2019), with the minor changes. pAG-Tn5 was used insted of pA-Tn5. pAG-Tn5 was constructed from pAG-MNase (addgene #123461) and pA-Tn5 (addgene #124601) plasmid DNAs. pAG sequence was excised from the pAG-MNase plasmid by digestion with EcoRI-HindIII. The pAG fragment was integrated into the Tn5 vector in which pA sequence was removed. ESCs and EB from either Pcgf1-KO or Ring1a/b mutant were dissociated by Accumax (Innovative Cell Technologies. For each assay, 100,000 cells were used with 10,000 cells of HEK293T as spike-in control.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: CUT&Tag
Sequencing was performed with 50x2 bp pair-end reads by NovaSeq6000 (run in RIKEN-IMS NGS facility) or 75x2 bp pair-end read by NextSeq500 (run by Kazusa DNA Research Institute).
Paired-end fastq data were aligned to UCSC mm9-hg38 reference genome by Bowtie2 2.3.2 with default option. Generated sam format file combine to bam format file using samtools view (version 1.3.1).
Then, PCR duplicate and multiple aligned reads are removed. For bigwig generation, bam format files were processed by deeptools bamCoverage (version 2.5.0.1 : --scaleFactor).
Spike-in scaling factor is calculated by the ratio of each human mapped reads and total reads.
Genome_build: mm9
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| Submission date |
Dec 04, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Hiroki Sugishita |
| E-mail(s) |
hiroki.sugishita@riken.jp
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| Organization name |
RIKEN
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| Department |
IMS
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| Lab |
Laboratory for Developmental Genetics
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| Street address |
1-7-22, Suehiro-cho
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| City |
Tsurumi-ku,Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE141486 |
Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [CUT&Tag] |
| GSE141488 |
Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes |
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| Relations |
| BioSample |
SAMN13482190 |
| SRA |
SRX7268297 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4204559_H2AK119ub_ERT2-Cre_Pcgf1Control_ES_rep2.bw |
102.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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