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Sample GSM1254295 Query DataSets for GSM1254295
Status Public on Oct 31, 2013
Title RICH
Sample type other
 
Source name ZM4 grown in a rich glucose medium (ZMRG)
Organism Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Characteristics media: rich ZRMG
temperature: 30C
Extracted molecule other
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
Description Mid-log phase in ZRMG, 1 biological replicate
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

Data table header descriptions
ID_REF
VALUE log2 level of mRNA at each location

Data table
ID_REF VALUE
PROBE_952919 11.4093909361377
PROBE_1903832 13.1444989258375
PROBE_1665364 12.0667619323869
PROBE_1407695 15.7797450000918
PROBE_1973827 8.07681559705083
PROBE_298281 11.698270577692
PROBE_715486 8.73131903102506
PROBE_1417898 8.16992500144231
PROBE_1702161 9.03342300153745
PROBE_1339167 9.91139198784346
PROBE_1976503 11.3420746679991
PROBE_371226 6.91886323727459
PROBE_1632732 8.07146236255662
PROBE_1901656 11.3761253892762
PROBE_29347 7.98299357469431
PROBE_393251 7.59245703726808
PROBE_537775 10.0794847838268
PROBE_1662351 11.2986354067342
PROBE_1677015 14.6079659767929
PROBE_335689 12.1241213118292

Total number of rows: 1870443

Table truncated, full table size 55429 Kbytes.




Supplementary file Size Download File type/resource
GSM1254295_7_30_11_slide382173_ZM4_til_RM_pmt300_532_border_minus1.ftr.gz 26.8 Mb (ftp)(http) FTR
Processed data included within Sample table

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