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| Status |
Public on Feb 02, 2019 |
| Title |
CdTe light 1 |
| Sample type |
SRA |
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| Source name |
exponential phase bacteria culture
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| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655 (ATCC700926)
media: M9 minimal medium
growth phase: exponential
treatment: 10 nM CdTe-2.4 quantum dot, LED illumination
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| Treatment protocol |
Nanoparticle concentration was held at 10 nM for both CdSe-2.4 and CdTe-2.4. The conditions, collected in biological duplicates, were as follows: no treatment, 10 nM CdTe-2.4 in light, 10 nM CdTe-2.4 in dark, 10 nM CdSe-2.4 in light, and 10 nM CdSe-2.4 in dark. The cells were treated for 5 hours.
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| Growth protocol |
Escherichia coli MG1655 (ATCC700926) was plated streaked from freezer stock onto lysogeny broth, agar plates (2% LB, 1.5% agar). Two individual colonies were selected and grown overnight in M9 minimal medium (1x M9 minimal media salts solution (MP Biomedicals), 2.0 mM MgSO4, 0.1 mM CaCl2, and 0.4% glucose). Cells were then diluted 1:100 into fresh M9 with respective treatment/illumination.
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 mL of culture was pelleted by centrifugation at 4,000 rpm for 10 min. Cell pellets described above we treated with Qiagen RNAprotect and flash frozen in a dry ice, ethanol bath for storage at -80C. RNA was then extracted using Thermo Scientific GeneJET RNA Purification Kit.
The RNA was then treated with Thermo Scientific TURBO DNA-free kit following the rigorous digestion protocol. Library preparation of the 10 samples (two biological replicates of five conditions) was done according to Shishkin et al (Shishkin et al., 2015). Sequencing was performed as 1x50, stranded, on three lanes in an Illumina HiSeq at the BioFrontiers Next Generation Sequencing facility at the University of Colorado Boulder. The three lanes generated an average of 126.7 million reads with a mean quality score of 35.7.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
bacterial mRNA
sample name in processed data file:
S3
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| Data processing |
Demultiplexing using fastq-multx in ea-utils v1.1.2
Trimmed low quality bases and Illumina adapters using Trimmomatic v0.32, settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
FASTQ files aligned to E. coli MG1655 genome (NCBI Reference Sequence NC_000913.3) using Bowtie2 v2.2.3 with "sensitive" settings
BAM files generated using Samtools v0.1.18
Count tables generated using HTSeq v0.6.1
Differential expression calculated using DESeq v3.4 using pooled replicates
Genome_build: NCBI genome assembly NC_000913/RefSeq Assembly GCF_000005845.2
Supplementary_files_format_and_content: Count tables for each condition, scaled to size factors generated by DESeq
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| Submission date |
Feb 01, 2019 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Thomas Aunins |
| E-mail(s) |
thau4793@colorado.edu
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| Phone |
2152909431
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| Organization name |
University of Colorado Boulder
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| Street address |
3460 Colorado Ave, B5
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| City |
Boulder |
| State/province |
CO |
| ZIP/Postal code |
80303 |
| Country |
USA |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE126008 |
Isolating the Escherichia coli transcriptomic responses to superoxide generation and stress from cadmium chalcogenide quantum dots |
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| Relations |
| BioSample |
SAMN10861499 |
| SRA |
SRX5323948 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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