strain: adhE*(EA) treatment: None substrate: Cellobiose 5g/L harvest time (hrs post treatment): 19
Treatment protocol
0.3 g/L acetate was added to CTFUD medium as a treatment.
Growth protocol
Ruminiclostridium thermocellum DSM 1313 adhE*(EA) was grown at 55 deg C in 27 ml Balch Tubes (10ml culture volume) in modified CTFUD medium.
Extracted molecule
total RNA
Extraction protocol
Briefly, samples were centrifuged and total cellular RNA was extracted by the TRIzol reagent (Invitrogen, Carlsbad, CA) and bead beating. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).
Label
Cy3
Label protocol
The labeling, hybridization, and scanning following NimbleGen company's protocols.
Hybridization protocol
The labeling, hybridization, and scanning following NimbleGen company's protocols.
Scan protocol
The labeling, hybridization, and scanning following NimbleGen company's protocols.
Description
27 mL Balch Tubes 10mL
Data processing
Microarrays were scanned with a SureScan High-Resolution DNA Microarray Scanner (5 μm) (Agilent), and the images were quantified using NimbleScan software (Roche NimbleGen, Madison, WI, USA). Raw data was log2 transformed and Loess normalized in JMP Genomics 5 (SAS Institute Inc., Cary, NC).
