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| Status |
Public on Sep 09, 2020 |
| Title |
S_2 |
| Sample type |
SRA |
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| Source name |
Control
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| Organism |
Staphylococcus aureus |
| Characteristics |
strain: ATCC43300
growth phase: planktonic
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from planktonic cells using an RNA prep pure bacteria kit (Beijing Tiangen, Cat: #DP430) .Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.
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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| Description |
Control
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
Supplementary_files_format_and_content: tab-delimited tex files include FPKM values for each samples
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| Submission date |
Sep 08, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
feng cheng |
| E-mail(s) |
cf1403@sina.com
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| Organization name |
Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agriculture Sciences
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| Street address |
335 Qilihe Rd,
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| City |
lanzhou |
| State/province |
GanSu |
| ZIP/Postal code |
730050 |
| Country |
China |
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| Platform ID |
GPL17452 |
| Series (1) |
| GSE157638 |
Integration of Metabolomics and Transcriptomics Reveals Changes in MRSA Exposed to Terpinen-4-ol |
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| Relations |
| BioSample |
SAMN16079391 |
| SRA |
SRX9090691 |
| 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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