|
| Status |
Public on May 27, 2011 |
| Title |
rich media DvH LS |
| Sample type |
RNA |
| |
|
| Source name |
DvH grown in lactate/sulfate media supplemented with yeast extract (LS)
|
| Organism |
Nitratidesulfovibrio vulgaris str. Hildenborough |
| Characteristics |
media: LS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes. Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment. RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used. Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.
|
| Label |
Alexa 555
|
| Label protocol |
First-strand cDNA was synthesized with random hexamer primers using SuperScript indirect cDNA labeling system (Invitrogen); the reaction buffer was supplemented with actinomycin D to inhibit second-strand synthesis. First-strand cDNA was labeled with Alexa 555. About 2 ug of labeled first-strand cDNA was hybridized to the array. For the genomic control, we used DNA from cells in stationary phase to minimize copy number variation across the chromosome. Genomic DNA was extracted using the DNeasy blood tissue kit (Qiagen) and labeled with Nimblegen's comparative genomic hybridization protocol. Briefly, genomic DNA was sonicated to 200-1000 bp and amplified using Klenow fragment and Cy3-labeled random nonamer primers.
|
| |
|
| Hybridization protocol |
Slides were hybridized using Nimblegen's standard protocol.
|
| Scan protocol |
Nimblegen slides were scanned on an Axon Gene Pix 4200A scanner with 100% gain
|
| Description |
Mid-log phase DvH in LS, 2 biological replicates
|
| Data processing |
Slides were analyzed with Nimblescan, with no local alignment and a border value of -1. Data from potentially cross-hybridizing probes (matching at 50 or more of 60 nucleotides to a second location in the genome) was removed.
|
| |
|
| Submission date |
May 26, 2011 |
| Last update date |
May 27, 2011 |
| Contact name |
Morgan N Price |
| E-mail(s) |
morgannprice@yahoo.com
|
| Organization name |
Lawrence Berkeley Lab
|
| Department |
Physical Biosciences Division
|
| Lab |
Arkin group
|
| Street address |
1 Cyclotron Road Mailstop 977-152
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL13654 |
| Series (2) |
| GSE29556 |
Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough (tiling array) |
| GSE29560 |
Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough |
|
