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Status |
Public on Oct 20, 2016 |
Title |
ChIP_hBMAL1 Chip-seq |
Sample type |
SRA |
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Source name |
U2OS cells
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Organism |
Homo sapiens |
Characteristics |
strain: ATCC HTB-96 tissue: bone genotype: osteosacoma chip antibody: hBMAL1 bethyl A302-616A
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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 |
genomic DNA |
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 |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
using standard protocol as cited in the paper (Cell. 2013 May 9;153(4):855-68)
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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 |
GPL16791 |
Series (1) |
GSE69100 |
Reciprocal Regulation between the Circadian Clock and Hypoxic Signaling in Mammals |
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Relations |
BioSample |
SAMN03703223 |
SRA |
SRX1034771 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1692868_ChIP_hBMAL1.bw |
116.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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