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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 28, 2021 |
| Title |
20-091 clinical |
| Sample type |
SRA |
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| Source name |
Bacterial colony
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| Organism |
Streptococcus equi subsp. equi |
| Characteristics |
disease state: Clinical
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| Growth protocol |
Streptococcus equi subsp. equi was grown in Todd Hewitt broth for 4 hours (exponential phase growth) at 37°C in 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RiboPure™ RNA Purification kit (Invitrogen™, Carlsbad, CA, USA) for bacteria, following the manufacturer’s instructions.
RNA libraries were prepared using the Stranded Total RNA Preparation kit (Illumina©, San Diego, CA, USA) following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Transcripts were trimmed using Trimmomatic
Alignment and transcript counts were performed using Salmon against the Streptococcus equi 4047 reference genome
Differential gene expression analysis was performed using edgeR, by the quasi-likelihood negative binomial generalized log-linear model
Genome_build: https://bacteria.ensembl.org/Streptococcus_equi_subsp_equi_4047_gca_000026585/Info/Index/
Genome_build: 553482
Supplementary_files_format_and_content: Salmon's quant.sf.txt - plain-text, tab-separated file
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| Submission date |
Feb 27, 2021 |
| Last update date |
May 28, 2021 |
| Contact name |
Ellen Ruth Alexander Morris |
| E-mail(s) |
ellenruth@tamu.edu
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| Organization name |
Texas A&M University
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| Street address |
TAMU 4475
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| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL29795 |
| Series (1) |
| GSE167862 |
RNA sequencing of Streptococcus equi subsp. equi collected from carrier and acute cases |
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| Relations |
| BioSample |
SAMN18082577 |
| SRA |
SRX10184318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5114083_20-091_quant.sf.txt.gz |
35.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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