|
| Status |
Public on Oct 31, 2013 |
| Title |
GENOMIC |
| Sample type |
genomic |
| |
|
| Source name |
GENOMIC
|
| Organism |
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 |
| Characteristics |
sample type: gDNA control
|
| Extracted molecule |
genomic DNA |
| 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 that bind to 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
|
| 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. Probes with low intensity in the genomic control (5th percentile or lower) were also removed.
|
| |
|
| Submission date |
Oct 29, 2013 |
| Last update date |
Oct 31, 2013 |
| 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 |
GPL17859 |
| Series (1) |
| GSE51870 |
High-resolution “tiling” expression data for Zymomonas mobilis ZM4 |
|
