7 protocols
AccessionType
normalization data transformation protocol
LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal. ID_REF = VALUE = log2 ratio (Cy5/Cy3) representing test/reference of the LOWESS normalized data PRE_VALUE = ratio (Cy5/Cy3) representing test/reference of the LOWESS normalized data
array scanning protocol
Scanned on an GenePix 4000A scanner. Images were analyzed using the programs Spotfinder (v321win) and Midas (v2.20).
hybridization protocol
Hybridization was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html
labelling protocol
Microbial RNA Aminoallyl Labeling was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html
growth protocol
S. sanguinis Δssa_1972 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic condition at 37 °C. Over night culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.
nucleic acid extraction protocol
Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions
growth protocol
S. sanguinis SK36 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic condition at 37 °C. Over night culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.