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| Status |
Public on Apr 01, 2012 |
| Title |
E. coli recoded ompF (recoded ompF gene) |
| Sample type |
SRA |
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| Source name |
E. coli recoded ompF
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| Organism |
Escherichia coli |
| Characteristics |
treatment: Ribosome-protected mRNA, Ribosome footprint sample digested with 60 units of micrococcal nuclease per A260 absorbance
strain: BJW9 w/ recoded ompF
medium: MOPS
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome protected mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ribosome-protected mRNA
Ecoli_ompF_recoded
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| Data processing |
After each sequenced fragments were aligned to the reference genome using Bowtie, the position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. More at G.W. Li, E. Oh, and J.S. Weissman, Nature (in press)
Genome Build:
OmpFrecode_f.wig: NC_000913.2
OmpFrecode_r.wig: NC_000913.2
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| Submission date |
Feb 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gene-Wei Li |
| E-mail(s) |
gene-wei.li@ucsf.edu
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| Organization name |
UCSF
|
| Street address |
1700 4th Street, BH404
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE35641 |
The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria |
|
| Relations |
| SRA |
SRX119214 |
| BioSample |
SAMN00783873 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM872399_OmpFrecode_f.wig.gz |
6.8 Mb |
(ftp)(http) |
WIG |
| GSM872399_OmpFrecode_r.wig.gz |
7.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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