4 X 72K probes Nimblegen microarray. For the probe design we used the Oligowiz software (Wernersson and Nielsen, 2005) and a reference pangenome composed of a representative sequence for each gene cluster to build a repertoire of possible isothermal probes of length between 45 nt and 65 nt. A relatively high target melting temperature 90°C (+/- 5°C) was selected to account for the high G+C-content of Pf (67%). Then, we proceeded to the probe selection according to two criteria. First, we required at least 45 nt between the 5'-ends of two adjacent probes on the reference sequence (implying the overlap to be less than 20 nt). Second, we preferred probes corresponding to genomic regions without SNPs and discarded all probes whose sequences contained more than two mismatches between any of the 8 genomes and the reference pangenome. When SNPs existed, we included in the design a perfect match variant for each probe allele in the 8 genomes, and only perfect match variant was used to measure gene expression. For technical reasons, probes requiring more than 148 synthesis cycles were also filtered out. Finally, all probes were duplicated.
Description
Propionibacterium freudenreichii strains CIRM121, CIRM122, CIRM129, CIRM134, CIRM139, CIRM456, CIRM514, and CIRM516. The design allows to monitor the expression of 2,740 genes (clusters) based on probing 27,546 distinct genomic regions (only 594 genes found in at least 1 of the 8 strains were not covered). On average, the expression of a gene was monitored via 10 distinct probe sequences (corresponding to 20 measures of intensity since each probe was duplicated). 120412_Pfreundenreichii_VL_exp.ndf 120412_Pfreundenreichii_VL_exp_X4.ncd
Transcriptome profiling of Propionibacterium freudenreichii strains associated with different anti-inflammatory properties.
Data table header descriptions
ID
A unique identifier for intensity measurements based on perfect match variants of the probe. This idenfifier is built by combining the PROBEGROUP_ID and the BLOCK
CDS_ID
A unique internal idenfier for each family of CDSs of the pangenome.
ORF
The locus_tag of a representatibe of the CDS family found in one of the 8 genomes (Genbank assembly number is provided in the sample information)
PROBEGROUP_ID
A unique identifier for the group of probes targeting a particular region of a CDS family alignment (this identifier combines the information of CDS_ID with the coordinates of the region in the alignment). If polymorphism exists in this region the group of probes contains one version per allelic sequence (perfect match variants). Otherwise, the group contains one unique version of the probe.
BLOCK
The block of the array; each probe in duplicated (ie appears in BLOCK1 and BLOCK2).
NSTRAINS
The number of strains in which the CDS queried by this probe is found.
PROBE_ID_CIRM121
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 121. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM122
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 122. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM129
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 129. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM134
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 134. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM139
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 139. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM456
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 456. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM514
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 514. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
PROBE_ID_CIRM516
Identifier of the perfect match probe corresponding to this PROBEGROUP_ID in Propionibacterium freudenreichii CIRM-BIA 516. It refers to PROBE_ID column of 120412_Pfreundenreichii_VL_exp.ndf and PAIR files.
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