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| Status |
Public on Dec 31, 2015 |
| Title |
nascent_RNA-peak-rep1 RNA-seq |
| Sample type |
SRA |
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| Source name |
U2OS cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS (ATCC HTB-96)
cell type: bone osteosarcoma
chip antibody: brdu antibody (sc-32323)
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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 |
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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
brdu-antibody aided
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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 |
GPL16791 |
| Series (1) |
| GSE68416 |
BMAL1 Activates Clock Gene Expression by Regulating Transcription Initiation |
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| Relations |
| BioSample |
SAMN03573823 |
| SRA |
SRX1014113 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1671336_nascent_RNA-peak-rep1.bedGraph.gz |
81.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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