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| Status |
Public on Apr 26, 2016 |
| Title |
Aerobic 3 |
| Sample type |
SRA |
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| Source name |
Cultured cells
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| Organism |
Escherichia coli |
| Characteristics |
strain: REL4536
growth phase: Stationary phase
growth environment: Aerobic
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| Growth protocol |
Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform at BGI (Shenzen, China).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs
The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤ Q28 were trimmed using Trim Galore! (Krueger F, 2013 ).
Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences.
RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters
Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and Anders S, 2014)
Genome_build: Escherichia coli B str. REL606; NC_012967.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample
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| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christina Moon |
| E-mail(s) |
christina.moon@agresearch.co.nz
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| Organization name |
AgResearch Ltd
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| Street address |
Tennent Drive
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| City |
Palmerston North |
| ZIP/Postal code |
4472 |
| Country |
New Zealand |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE80451 |
Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically |
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| Relations |
| BioSample |
SAMN04870309 |
| SRA |
SRX1714423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2127619_AE3_rpkm.txt.gz |
85.6 Kb |
(ftp)(http) |
TXT |
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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