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| Status |
Public on Jul 30, 2017 |
| Title |
WT 5min rep6 |
| Sample type |
SRA |
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| Source name |
cell culture
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| Organism |
Escherichia coli |
| Characteristics |
infection: T7
t7 strain: wild type
t7 genotype: wild-type gene 10
time: 5 min post-infection
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol reagent (Thermo Fisher Scientific)
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
pseudoalignment and quantitation with kallisto v0.42.5 with parameters --single -l 450 -s 250
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes, and with recoded gene 10 sequence (Bull, 2012, PMCID: PMC3457771) in place of wild-type sequence for analysis of recoded and evolved strains
Supplementary_files_format_and_content: tab-delimitted text files contain TPM (transcripts per million) values for each sample
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| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Claus Wilke |
| Organization name |
University of Texas at Austin
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| Department |
Integrative Biology
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| Lab |
Wilke
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| Street address |
2500 Speedway, A4800
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| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL21222 |
| Series (1) |
| GSE96573 |
Reduced protein expression in a virus attenuated by codon deoptimization |
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| Relations |
| BioSample |
SAMN06569077 |
| SRA |
SRX2637803 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2536128_PA43-wild10A-46-1min-rep2.tsv.gz |
80.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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