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| Status |
Public on Dec 31, 2018 |
| Title |
DMSO |
| Sample type |
SRA |
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| Source name |
cj9 mES cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
treatment: DMSO
strain: 129/Ola
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| Treatment protocol |
The cells were treated with DMSO, Actinomycin D (1ug/ml) and DRB (100uM) for 2hrs
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| Growth protocol |
Wild-type (cj9) and infected embryonic stem cells (ESCs) were cultured on gelatin coated plates in standard ESC medium consisting of DMEM (Cellgro) supplemented with 15% heat-inactivated fetal bovine serum (Hyclone), 1% Glutamax (GIBCO), 1% Penicillin/Streptomycin (Cellgro), 1% nucleoside (Millipore), 0.1mM 2-mercaptoethanol (GIBCO), 1% MEM nonessential amino acids (Cellgro), and 1000U/ml recombinant leukemia inhibitory factor (Millipore).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Treated cells (4X15 cm dishes) were harvested by trypsinization and rinsed twice by PBS. Then the cells were treated by 10ml Buffer A (10mM Hepes, pH 7.9, 10mM KCl, 1.5mM MgCl2, 0.5mM DTT) on ice for 5min followed by 10X Dounce homogenization. Centrifuge the cells at 218g for 5min at 4C. Then resuspend the pellet with 3 ml S1 solution (0.25M sucrose, 10mM MgCl2) and layered over 3ml S2 solution (0.35M sucrose, 0.5mM MgCl2) and centrifuged at 1430g for 5min at 4C. Resuspend the pellet with 3ml of S2 solution and sonicate to break the nuclei. Layered the sonicated sample over 3ml of S3 solution (0.88M Sucrose, 0.5mM MgCl2) and centrifuge at 3000g for 10min at 4 C. Resuspended the nucleoli with 500ul of S2 solution and centrifuged for another 5min. The pellet was resuspended and purified by phenol-chloroform extraction.
Nucleolar retrieved DNA-seq were prepared by library preparation modules (New England Biolabs)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
Nucleolar retrieved DNA-Seq reads were aligned to the mm10 genome assembly using Bowtie2 version 2.2.3 with the default parameters
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Sep 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
jinlong lu |
| E-mail(s) |
bioyuyang@hotmail.com
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| Phone |
5853098469
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| Organization name |
University of Rochester
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| Lab |
Gorbunova & Seluanov Labs
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| Street address |
213 Hutchinson Hall
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14627 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
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| Relations |
| BioSample |
SAMN07615462 |
| SRA |
SRX3168119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2776415_DMSO_L3_A002.all.align.sam.sort.bw |
207.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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