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| Status |
Public on Dec 31, 2020 |
| Title |
Fermentation liquid, S23 |
| Sample type |
SRA |
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| Source name |
Fermentation liquid
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| Organism |
Serratia marcescens |
| Characteristics |
strain: JNB 5-1
treatment: 37C
time of sampling: 24h
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| Treatment protocol |
After incubating JNB 5-1 at 30C and 37C for 22 hours, the growth temperature of 2 bottles was interchanged to continue the cultivation, and the remaining 2 bottles continued to be cultured at the original temperature until 36h. Total RNA was sampled at 12h and 24h, at 36h, respectively, and sequenced to analyze the effect of temperature on PG production by S. marcescens. In order to distinguish the samples, we named the samples S11, S12, S13, S14, S21, S22, S23, S24, S31, S32, S33, S34. S11, S12, S13, S14 were sampled at 12h (T12). S21, S22, S23, S24 were sampled at 24h (T24), S21 was converted from 30C to 37C and S24 was converted from 37C to 30C at 22h. S31, S32, S33 and S34 were sampled at 36h (T36), S31 was converted from 30C to 37C and S34 was converted from 37C to 30C at 22h.
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| Growth protocol |
Incubating JNB 5-1 at 30C and 37C in LB medium
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using an RNeasy kit (Vazyme, Nanjing, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（ 5X） . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（ RNaseH-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 µl USER Enzyme (NEB， USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v2.2.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq software to analyze the gene expression level of each sample, and the model used was union.
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP005927.1
Supplementary_files_format_and_content: .txt file reports RPKMs
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| Submission date |
Feb 02, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
YANG SUN |
| E-mail(s) |
[email protected]
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| Organization name |
JIANGNAN UNIVERSITY
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| Street address |
LIHU ROAD
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| City |
WUXI |
| ZIP/Postal code |
214000 |
| Country |
China |
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| Platform ID |
GPL28109 |
| Series (1) |
| GSE144646 |
Insight into the regulation of prodigiosin production by temperature in Serratia marcescens through transcriptome analysis |
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| Relations |
| BioSample |
SAMN13968911 |
| SRA |
SRX7660413 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4292828_S23.txt.gz |
43.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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