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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2018 |
| Title |
V6.5 Control [MNase-Seq] |
| Sample type |
SRA |
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| Source name |
V6.5 Control
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| Organism |
Mus musculus |
| Characteristics |
cell line: V6.5
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HeLa cells (3X105) were treated with either scrambled siRNA, or RNF2 siRNA, or RSF1 siRNA. 48 hrs later, cells were harvested and total RNA was extracted with Trizol. For mouse ESC, total RNA was extracted directly from wild type and RSF1 KO cells. For ChIP sequencing experiments, ChIP was performed with anti-FLAG antibody in a mouse ESC line stably expressing FLAG-RSF1.
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP and Mnase libraries were prepared for sequencing using standard illumina protocols
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
MnaseSeq
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to remove adapters and low quality bases
Reads were mapped to mm10 or hg19 with TopHat (tophat -p 12 --mate-inner-dist=200 --mate-std-dev=40 --no-mixed --no-coverage-search) for RNAseq or BWA samse for ChIPseq
Transcripts were assembled with Cufflinks.
Differential gene expression was performed by Cuffdiff
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Gene expression values are a direct output of Cuffdiff. Bedgraph files were scaled to 10 million reads
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| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hengbin Wang |
| Organization name |
Virginia Commonwealth University
|
| Department |
Massey Cancer Institute
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| Street address |
401 College Street
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| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE83360 |
Investigation of Rsf1 genomic distribution and effect on gene expression |
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| Relations |
| BioSample |
SAMN05249977 |
| SRA |
SRX1845480 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2200234_negative_control_nucleosome.bedgraph.gz |
799.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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