ERP015160
Study Detail
| Title | Global gene expression of EHEC O26:H11 21765 and O157:H7 EDL933 strains in ground beef with or without microflora |
| Study Type | Other |
| Abstract | The genomic expression profiles of enterohemorrhagic Escherichia coli O26:H11 21765 and O157:H7 EDL933 strains grown in ground beef enriched in microflora were compared with the corresponding expression profiles in ground beef without microflora. For our application of RNA-Seq, 3 biological replicat .. [more]es were performed. To reduce the possibility of spurious alignment and crosstalk between the reference genome of EHEC and other similar genomes, the transcriptionally up-regulated genes in presence of microflora were filtered for E. coli specific genes. This constraint also influenced our sequencing strategy, sequencing mode (paired-end sequencing), library-type (strand-specific cDNA library) and choice of the read length (125 bp). The paired-end strand-specific RNA-Seq with a read length of 125 bp informations allow for higher levels of specific alignments, thus reduce the possibility of spurious alignment between the reference genome and other similar genomes. [less] |
| Description | The genomic expression profiles of enterohemorrhagic Escherichia coli O26:H11 21765 and O157:H7 EDL933 strains grown in ground beef enriched in microflora were compared with the corresponding expression profiles in ground beef without microflora. For our application of RNA-Seq, 3 biological replicat .. [more]es were performed. To reduce the possibility of spurious alignment and crosstalk between the reference genome of EHEC and other similar genomes, the transcriptionally up-regulated genes in presence of microflora were filtered for E. coli specific genes. This constraint also influenced our sequencing strategy, sequencing mode (paired-end sequencing), library-type (strand-specific cDNA library) and choice of the read length (125 bp). The paired-end strand-specific RNA-Seq with a read length of 125 bp informations allow for higher levels of specific alignments, thus reduce the possibility of spurious alignment between the reference genome and other similar genomes. [less] |
| Center Name | VETAGROSUP |
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Submission | ERA609436 |
 FTP
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| ERA610479 |
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| ERA612558 |
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Experiment | ERX1442034 |
FASTQ
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SRA
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| ERX1442035 |
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| ERX1442036 |
FASTQ
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| ERX1442037 |
FASTQ
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| ERX1442038 |
FASTQ
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| ERX1442039 |
FASTQ
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SRA
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| ERX1442040 |
FASTQ
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SRA
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| ERX1442041 |
FASTQ
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SRA
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| ERX1442042 |
FASTQ
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SRA
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| ERX1442043 |
FASTQ
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SRA
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| ERX1442044 |
FASTQ
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SRA
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| ERX1442045 |
FASTQ
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SRA
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| ERX1460015 |
FASTQ
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SRA
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| ERX1468730 |
FASTQ
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Sample | ERS1127228 | ||
| ERS1127229 | ||||
| ERS1127230 | ||||
| ERS1127231 | ||||
| ERS1127232 | ||||
| ERS1127233 | ||||
| ERS1127234 | ||||
| ERS1127235 | ||||
| ERS1127236 | ||||
| ERS1127237 | ||||
| ERS1127238 | ||||
| ERS1127239 | ||||
| ERS1133543 | ||||
| ERS1138027 |