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Status |
Public on Dec 31, 2015 |
Title |
BM-H3K27ac Chip-seq |
Sample type |
SRA |
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Source name |
MEF cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: embryonic-fibroblast genotype: bmal1-/- chip antibody: H3K27ac (Active Motif, 39133)
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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 |
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq RNA-seq: For MEF cell line and U2OS cell line mRNA-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: ChIP-seq procedure as previously described (34, 35). For the Bmal1 ChIP-seq, the RIPA buffer was diluted 1 to 10 and 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
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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: bedGraph files for RNA-seq and chip-seq
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Submission date |
Apr 29, 2015 |
Last update date |
May 15, 2019 |
Contact name |
xiong will wei |
E-mail(s) |
xiongwei@nibs.ac.cn
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Organization name |
NIBS,Beijing
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Street address |
7 Science Park Road ZGC Life Science Park
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City |
Beijing |
ZIP/Postal code |
102206 |
Country |
China |
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Platform ID |
GPL17021 |
Series (1) |
GSE68416 |
BMAL1 Activates Clock Gene Expression by Regulating Transcription Initiation |
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Relations |
BioSample |
SAMN03573810 |
SRA |
SRX1014100 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1671323_BM-H3K27ac.bedGraph.gz |
7.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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