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| Status |
Public on Sep 26, 2017 |
| Title |
sp2 |
| Sample type |
SRA |
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| Source name |
Broiler Fecal
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| Organism |
Escherichia coli |
| Characteristics |
strain: Poultry E. coli Virulent and multidrug resistant
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| Treatment protocol |
No treatment
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| Growth protocol |
Strains were harvested in MH broth at log phase
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from the bacterial isolates using TRIzol
Following "TruSeq RNA Sample Preparation Guide".
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
RNA-Seq of E. coli were done using blind and fit-only parameter in DE-Seq pakage
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
first strand cDNA was performed by the use of SuperScriptII and the second strand cDNA synthesis was done before end-pair and dA-tailing
Reads longer than 25 nt and ≤ 2 N (ambiguous nucleotides) were preserved.
Using blind and fit-only parameter in DE-Seq pakage, expressions of genes in all samples were changed to count per gene, using RNA-Seq protocol on Illumina HiSeq2500 platform
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
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| Submission date |
Feb 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ganlin Xu |
| E-mail(s) |
634697641@qq.com
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| Phone |
18826232430
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| Organization name |
shbiochip
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| Street address |
CB
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| City |
Guangzhou |
| ZIP/Postal code |
shbiochip |
| Country |
China |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE94978 |
Comparative Transcriptomic Profiling of Antimicrobial Resistant and Virulent Escherichia coli of Poultry Origin |
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| Relations |
| BioSample |
SAMN06341141 |
| SRA |
SRX2566818 |
| 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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