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| Status |
Public on Oct 20, 2016 |
| Title |
RNAseq_WT-P RNA-seq |
| Sample type |
SRA |
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| Source name |
MEF cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: embryonic-fibrobalst
genotype: circadian trough wildtype
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| Treatment protocol |
serum shock the MEF cell for 24h (circadian peak) and 36h (circadian trough)
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| Growth protocol |
DMEM plus 10% for both MEF and U2OS cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using a RNeasy MinElute Cleanup Kit
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L). For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629). For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA. Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
oligoT matrix facilitated
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| Data processing |
FASTX-Toolkit for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigwig files for RNA-seq and chip-seq
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| Submission date |
May 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
xiong wei |
| E-mail(s) |
1301110432@pku.edu.cn
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| Organization name |
peking university
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| Street address |
5 Yiheyuan Rd, Haidian, Beijing, China
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE69100 |
Reciprocal Regulation between the Circadian Clock and Hypoxic Signaling in Mammals |
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| Relations |
| BioSample |
SAMN03703228 |
| SRA |
SRX1034776 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1692873_RNAseq_WT-P.bw |
63.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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