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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 26, 2019 |
| Title |
PAR48-JARID2 |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: JARID2
library strategy: ChIP-seq
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| Treatment protocol |
Indicated cells were treated for 72 h with 0.5 μM 4-hydroxytamoxifen (OHT; or EtOH as vehicle) in order to delete Ring1b gene
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| Growth protocol |
mESCs were grown on 0.1% gelatin-coated dishes in 2i/LIF-containing GMEM medium (Euroclone) supplemented with 20% fetal calf serum (Euroclone), 2 mM glutamine (Gibco), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 50 µM ß-mercaptoethanol phosphate buffered saline (PBS; Gibco), 1000 U/ml leukemia inhibitory factor (LIF; produced in-house), and GSK3β and MEK 1/2 inhibitors (ABCR GmbH) to a final concentration of 3 mM and 1 mM, respectively
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed according to standard protocols as described previously (Ferrari et al., 2014)
DNA libraries were prepared with 2–10 ng of DNA using an in-house protocol (Blecher-Gonen et al., 2013) by the IEO genomic facility
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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 |
Paired-end reads were aligned to the mouse reference genome mm10, or mm10 and dm6 for histone ChIP-Rx, using Bowtie v1.2.2 (Langmead et al., 2009) without allowing for multi-mapping (–m 1) and parameters -I 10 -X 1000. PCR duplicates were removed using samblaster (Faust and Hall, 2014). Ambiguous reads mapping to both mm10 and dm6 were discarded. Peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with parameters -f BAMPE --keep-dup all -m 10 30 -p 1e-10.
Reads were aligned to the mouse reference genome mm10 using STAR v2.7 without allowing multimapping reads (--outFilterMultimapNmax 1). PCR duplicates were removed using samblaster (Faust and Hall, 2014). Gene counts were calculated using featureCounts (Liao et al., 2014) with parameters -s 0 -t exon -g gene_name using Gencode M21 (GRCm38) annotation downloaded from (https://www.gencodegenes.org/mouse/). Differential expression analyses were performed using the R package DESeq2 v1.20 (Love et al., 2014) using default parameters. Log2FoldChanges and adjusted p-values were corrected using the apeglm (Zhu et al., 2019) and IHW (Ignatiadis et al., 2016) packages, respectively. Genes with an absolute log2 fold change of 1.5 and FDR < 0.05 were considered as differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: counts.tsv : raw counts, Normalized_counts.tsv : normalized counts (DESeq2), Eed_OHT-vs-Eed_ETA_diffexp_log2fc1.5_pval0.05.tsv : differential expression results
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| Submission date |
Dec 20, 2019 |
| Last update date |
Dec 27, 2019 |
| Contact name |
Diego Pasini |
| E-mail(s) |
[email protected]
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| Organization name |
European Institute of Oncology
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| Street address |
Via Adamello, 16
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| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE134053 |
Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression |
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| Relations |
| BioSample |
SAMN13658898 |
| SRA |
SRX7423730 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4227586_PAR48-JARID2_E14-input_peaks_p10.bed.gz |
49.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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