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| Status |
Public on Sep 27, 2016 |
| Title |
Sample_2_A1 |
| Sample type |
SRA |
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| Source name |
S. equorum_alone
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| Organism |
Staphylococcus equorum |
| Characteristics |
strain: BC9
growth condition: alone
tissue: experimental biofilm
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| Treatment protocol |
Staphylococcus equorum was grown either alone, with a Penicillium spp., or with a Scopulariopsis spp.
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| Growth protocol |
Experimental biofilms were created by inoculating organisms onto cheese curd agar medium. See Wolfe et al. 2014 Cell 158 422-433
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a phenol-chloroform
RNA libraries were prepared using the NEBNext RNA Ultra Kit for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Staphylococcus equorum grown alone, Replicate 1
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| Data processing |
Basecalls performed using CASAVA
Transcripts were aligned to S. equorum BC9 draft genome (Accesson No. LNNB00000000) using Rockhopper Reference Assembly, using standard options: Strand-specific checked yes, max bases between paired reads: 500, allowed mismatches: 0.15, minimum seed length 0.33, minimum expression of UTRs and ncRNAs: 0.5,
Differential Gene expression and Operon identification performed by Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/)
Genome_build: Staphylococcus equorum BC9; LNNB00000000 private accession at NCBI Whole Genome Shotgun (WGS) archive
Supplementary_files_format_and_content: Rockhopper_analysis_FOR_GEO.xlsx
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| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin E Wolfe |
| E-mail(s) |
[email protected]
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| Organization name |
Tufts University
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| Department |
Microbiology
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| Street address |
200 Boston Ave.
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| City |
Medord |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
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| Platform ID |
GPL21188 |
| Series (1) |
| GSE75505 |
Differential expression of Staphylococcus equorum grown alone and in the presence of fungi |
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| Relations |
| BioSample |
SAMN04302104 |
| SRA |
SRX1456218 |
| 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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