|
| Status |
Public on Feb 01, 2017 |
| Title |
adhE*_Cellobiose_Acetate_2 |
| Sample type |
RNA |
| |
|
| Source name |
adhE* Cellobiose Acetate 2
|
| Organism |
Acetivibrio thermocellus DSM 1313 |
| Characteristics |
strain: adhE*(EA)
treatment: Acetate 0.3g/L
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).
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
Feb 01, 2017 |
| Contact name |
Jason Whitham |
| E-mail(s) |
whithamjm@ornl.gov
|
| Organization name |
Oak Ridge National Labs
|
| Street address |
1 Bethel Valley Rd Bld 1505 Rm 366 MS 6038
|
| City |
Oak Ridge |
| ZIP/Postal code |
37831 |
| Country |
USA |
| |
|
| Platform ID |
GPL18170 |
| Series (1) |
| GSE77273 |
Ruminiclostridium thermocellum DSM 1313 strain adhE*(EA) expression arrays |
|
