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| Status |
Public on Dec 03, 2024 |
| Title |
ATCC 8739, high pressure, 300 MPa, rep2 |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organism |
Escherichia coli |
| Characteristics |
cell type: bacterial cells
strain: ATCC 8739
treatment: high pressure processing, 300 MPa, 3 min
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| Growth protocol |
E. coli ATCC 8739 culture in LB medium at 37°C for 16±1 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy Mini Kit from Qiagen.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
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| Description |
Library name: H4B
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| Data processing |
Quantified libraries were pooled and sequenced on an Illumina platform NovaSeq X Plus Series
Raw data (raw reads) in FASTQ format was first processed through fastp
The cleaned reads were aligned to reference genome of E. coli ATCC 8739 (GCA_016864475.1) using Bowtie2
To count the reads numbers mapped to each gene, FeatureCounts was used
Differential expression analysis was performed using the DESeq2 R package, and the p-values were adjusted using the Benjamini and Hochberg’s approach to control the false discovery rate.
Assembly: Reference genome: GCA_016864475.1
Supplementary files format and content: csv files include FPKM values for each samples
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| Submission date |
Dec 02, 2024 |
| Last update date |
Dec 03, 2024 |
| Contact name |
Astrid Gedas |
| E-mail(s) |
[email protected]
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| Organization name |
Universität Hamburg
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| Department |
Department of Chemistry
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| Lab |
Food Microbiology
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| Street address |
Ohnhorststrasse 18
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| City |
Hamburg |
| ZIP/Postal code |
22609 |
| Country |
Germany |
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| Platform ID |
GPL34685 |
| Series (1) |
| GSE283248 |
Differential gene expression of Escherichia coli ATCC 8739 in strawberry nectar after thermal and non-thermal treatments |
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| Relations |
| BioSample |
SAMN45122727 |
| SRA |
SRX26930829 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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