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| Status |
Public on Jul 27, 2016 |
| Title |
N8D-70SIC |
| Sample type |
SRA |
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| Source name |
in vitro transcription
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| Organism |
Escherichia coli |
| Characteristics |
sample type: mRNAs N8D captured by ribosome 70S initiation complex
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| Extracted molecule |
total RNA |
| Extraction protocol |
Randomized mRNAs were recruited on ribosome at the different initiation complex by incubation of the initiation reaction at 37oC for 30 min until initiation complex to reach equilibrium. Initiation complexes were collected using Ni-NTA chromatography to capture the his-tagged ribosomal protein followed by phenol:chloroform treatment to remove all the ribosomal proteins. Finally, the pools of RNAs were precipitated by ethanol, resuspended in distilled H2O, and used directly for sequencing library preparation. The RNA pools include both the ribosomal RNAs and the selected mRNAs binding to initiation complex.
The sequencing library was prepared by following the procedure described in NEBNext MultiplexSmall RNA Library Prep Set for Illumina.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8.
Using in-house python script, trim microRNA adapter sequence from reads, then filter out reads who have low quality scores.
Use a given sequence according to the experiment designment as an anchor, trim fixed sequences with in-house script, only keep the 'N' part.
For each sample's filted fasta file, summarize nucleotide occurance at each base, showed in Nucleotide_Statistic_Analysis.xlsx file. Base number means the position of the base in the randomized region from 5' end to 3' end.
Supplementary_files_format_and_content: Fasta format files of translational initiation region sequences.
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| Submission date |
Jun 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiao-Dong Su |
| E-mail(s) |
xdsu@pku.edu.cn
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| Phone |
861062759743
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| Organization name |
Peking University
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| Department |
School of Life Science
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| Street address |
No.5 Yiheyuan Road, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE69782 |
Deep sequencing reveals mRNA recruitment in translation initiation |
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| Relations |
| BioSample |
SAMN03769958 |
| SRA |
SRX1056612 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1708733_B2-N8D-4-getN.fa.gz |
10.4 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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