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| Status |
Public on Apr 04, 2016 |
| Title |
wt20_RNA-Seq |
| Sample type |
SRA |
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| Source name |
mouse embryonic fibroblast cells
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| Organism |
Mus musculus |
| Characteristics |
circadian time: CT20
genotype: wild type
treatment: Dexamethesone synchronization
cell type: MEF
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| Extracted molecule |
total RNA |
| Extraction protocol |
Smc3-flox/flox MEF (mouse embryonic fibroblast) cells was originally derived from European conditional mouse mutagenesis program (White et al., 2013) (http://www.informatics.jax.org/allele/MGI:4434007). The Cre/GFP adenovirus and GFP adenovirus were purchased from Hanbio biotechnology Shanghai. MEF cells were cultured with 10% FBS in DMEM (Life technology). To avoid loss of viability in Smc3-deficient cells when they enter mitosis, we infected the cells at G0/1 stage of the cell cycle. The medium was changed two days after complete confluence. 10e9 pfu GFP and Cre/GFP adenovirus were used in 8-hr treatment for wild type and Smc3-/- MEF cells respectively. To allow cells to recover from viral infection, we changed the medium into serum-free DMEM and kept cells for 6 days at high confluence. MEF cells were then synchronized by dexamethasone (Sigma) with the final concentration of 100 nM for 1 hour. The cells were rinsed with PBS and cultured with serum-free DMEM. Wild type and Smc3 KO MEF cells were collected at 20, 24, 28, 32, 36, and 40 hr after synchronization. Total RNA in CT20 and CT32 samples were extracted using Trizol reagent and reverse-transcribed into cDNA by SuperScript II RT (Life Technologies). RNA-seq libraries were prepared by using Illumina TruSeq RNA Sample Prep Kit V2 and were subjected to deep sequencing with 100 bp read on HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequencing reads were mapped to mouse reference genome (mm9 essembly) by Tophat1.4 with default parameters.
HTSeq0.6 was applied to count the number of uniquely mapped reads that locate on the exons of genes. Only genes with at least one read in all samples were kept for downstream analysis.
DESeq3.1 was used to select differentially expressed genes between wild type and knockout.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include reads count of genes. The 1st column is gene symbol and the 2nd column is the number of reads mapped to exons of the gene.
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| Submission date |
May 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yichi Xu |
| E-mail(s) |
xuy2@mskcc.org
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| Organization name |
MSKCC
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| Street address |
1275 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE68831 |
Long-range chromosome interactions mediated by cohesin shape circadian gene expression [RNA-Seq] |
| GSE68832 |
Long-range chromosome interactions mediated by cohesin shape circadian gene expression |
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| Relations |
| BioSample |
SAMN03656199 |
| SRA |
SRX1024671 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1682610_wt20_count.txt.gz |
92.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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