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| Status |
Public on Jun 09, 2024 |
| Title |
H4T71Gc_hES_ChIP-seq |
| Sample type |
SRA |
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| Source name |
H4T71Gc_hES
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| Organism |
Homo sapiens |
| Characteristics |
treatment: normal condition
cell type: Undifferentiated embryonic stem cells
chip-antibody: 20H3 (mouse monoclonal antibody, prepared in-house)
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| Treatment protocol |
mESCs were cultured in ES medium containing 25 mM (normal condition, HG-mESCs) or 1 mM glucose (LG-mESCs) for 96 hrs.
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| Growth protocol |
mESCs line J1, derived from 129S4/SvJae mouse embryos, were maintained the stemness on the gelatin-coated dish in D-MEM (Wako) supplemented 20% fetal bovine serum, 2 mM L-glutamine (Wako), 1 mM Na-pyruvate (Wako), Non-essential amino acid (Wako), 0.1 mM 2-Mercaptoethanol (Wako), Penicillin-Streptomycin (Wako) and 1,500 U/mL LIF (ESGRO; Millipore). Glucose concentration was adjusted using 2.5 M glucose solution (Sigma-Aldrich) to 1 or 25 mM. hiPSCs line 201B7 were also maintained the stemness on feeder layers of mitomycin C-treated STO/Neo resistant/LIF (SNL) feeder cells in ReproStem medium (ReproCELL) supplemented with 5 ng/mL bFGF (Wako). The pellets of fixed hESCs line H9 maintained the stemness was provided by Dr. Suzuki (University of Wisconsin, Madison).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, 53009) and H4T71Gc specific antibody (20H3) according to the manufacturer’s instructions. For repairing the ends of DNA fragments isolated by ChIP (50 ng each), adding a single “A” base to the 3’-end of them, and ligating TruSeq DNA adapters (illumina) to them,KAPA hyper Prep kit (KAPA Biosystems) was used according to the manufacturer’s instructions. Ligation products were purified on KAPA pure beads (KAPA Biosystems) to remove unligated adapters and subjected to eight cycles of PCR amplification. Completed libraries were quantified using Library Quantification Kit (Takara bio).
In this study, all of data processing for ChIP-seq was performed by using Galaxy platform (https://usegalaxy.org/). ChIP-seq reads were mapped to mm10 assembly of mouse genome or hg38 assembly of human genome using Bowtie2. The peaks of all samples were detected using MACS. The following parameter was used: input-seq aligned reads as a control file, 25 bp tag size, 300 bp bandwidth, and 10e-03 (for mouse) or 10e-05 (for human) p-value cutoff for peak detection.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
ChIP-seq reads were mapped to mm10 assembly of mouse genome or hg38 assembly of human genome using Bowtie2 (v2.3.4.2).
The peaks of all samples were detected using MACS (v1.0.1). The following parameter was used: input-seq aligned reads as a control file, 25 bp tag size, 300 bp bandwidth, and 10e-03 (for mouse) or 10e-05 (for human) p-value cutoff for peak detection.
The H4T71Gc coverage track normalized by input-seq in mESCs was generated by BamCompare (v3.1.2.0.0) using mapping data of H4T71Gc and input.
Genome_build: mm10 (Mus musculus), hg38 (Homo sapiens)
Supplementary_files_format_and_content: Bam files were generated by Bowtie2 (v2.3.4.2) analysis using each fastq data. Bed files and Bigwig files were generated by MACS (v1.0.1) and BamCompare (v3.1.2.0.0) analysis using each bam data of H4T71Gc ChIP-seq and Input-seq, respectively.
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| Submission date |
Jun 22, 2020 |
| Last update date |
Jun 09, 2024 |
| Contact name |
Daisuke Nara |
| Organization name |
The uniersity of Tokyo
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| Department |
Dep. of Animal resource sciences
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| Lab |
Lab. of cellular biochemistry
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| Street address |
1-1-1 Yayoi
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| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
1138657 |
| Country |
Japan |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE153008 |
Novel O-GlcNAcylation on Thr71 of histone H4 preferentially localizes to active gene regions |
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| Relations |
| BioSample |
SAMN15343872 |
| SRA |
SRX8598570 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4633020_hESC_H4T71Gc_MACS_peakcall.bed.gz |
447.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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