|
| Status |
Public on Oct 20, 2011 |
| Title |
Lodderomyces elongisporus Xylose Replicate 2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Lodderomyces elongisporus NRRL YB-4239 xylose
|
| Organism |
Lodderomyces elongisporus NRRL YB-4239 |
| Characteristics |
treatment: 2% xylose for 3 generations growth
|
| Treatment protocol |
One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.
|
| Growth protocol |
Lodderomyces elongisporus NRRL YB-4239 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase. Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures. Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture. Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414. Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen). RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).
|
| Label |
Cy5
|
| Label protocol |
Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion). RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.
|
| |
|
| Channel 2 |
| Source name |
Lodderomyces elongisporus NRRL YB-4239 genomic
|
| Organism |
Lodderomyces elongisporus NRRL YB-4239 |
| Characteristics |
treatment: Genomic DNA was extracted from cells growing in log phase
|
| Treatment protocol |
One culture was treated with 2% glucose for 3 generations growth; the other culture was treated with 2% xylose for 3 generations growth.
|
| Growth protocol |
Lodderomyces elongisporus NRRL YB-4239 was grown aerobically at 30˚C for approximately 16 h in YPD (1% yeast extract, 2% peptone, 2% glucose) to early-log phase. Cells were washed once in YP (1% yeast extract, 2% peptone) and split into two cultures. Both cultures received the addition of sugar to a final concentration of 2%: glucose was added to one culture; xylose was added to the other culture. Cells were collected at OD600 0.5-0.6 after 3 generations aerobic growth at 30˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell collection, lysis, and total RNA isolation were performed as previously described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414. Following total RNA isolation, RNA was further purified with LiCl and RNeasy Mini kit (Qiagen). RNA concentration was determined by NanoDrop spectrophotometer (Thermo Scientific).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed as described in Gasch, A. P. (2002) Methods Enzymol 350: 393-414, using cyanine dyes (Amersham), Superscript III (Invitrogen), and amino-allyl-dUTP (Ambion). RNA collected from cells grown in each sugar condition was labeled with Cy5 dye and was directly compared to a genomic DNA reference sample labeled with Cy3 dye.
|
| |
|
| |
| Hybridization protocol |
Arrays were hybridized in a NimbleGen hybridization system 12 (BioMicro) following the standard NimbleGen operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Arrays were scanned using a GenePix 4000B scanning laser (Molecular Devices) following the standard NimbleGen operating protocol. See www.nimblegen.com.
|
| Description |
Biological replicate 2 of 3. Experimental xylose-grown cells, harvested after 3 generations.
|
| Data processing |
Data normalization was performed using custom perl scripts and Bioconductor (Gentleman, R. C. et al. (2004) Genome Biol 5: R80). The affy() package (Gautier, L. et al. (2004) Bioinformatics 20: 307-315) was used to apply probe-level quantile normalization to the log2 signal of RNA versus the genomic DNA control (Cy5/Cy3). Gene-level expression changes were summarized with the median value of each probe set contained completely within each predicted ORF. See the included file LeloProbeMapping.txt for a mapping of probes to genes.
|
| |
|
| Submission date |
Oct 21, 2010 |
| Last update date |
Oct 20, 2011 |
| Contact name |
Dana Jasmine Wohlbach |
| E-mail(s) |
[email protected]
|
| Organization name |
Dickinson College
|
| Department |
Biology
|
| Street address |
P.O. Box 1773
|
| City |
Carlisle |
| State/province |
PA |
| ZIP/Postal code |
17013 |
| Country |
USA |
| |
|
| Platform ID |
GPL11081 |
| Series (2) |
| GSE24855 |
Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose |
| GSE24858 |
Expression analysis of various fungi grown in glucose or xylose |
|
