|
| Status |
Public on Oct 01, 2008 |
| Title |
293T New B, 2mM NaOH treatment |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Total RNA are from 293T cells, 2mM NaOH treated
|
| Organism |
Homo sapiens |
| Characteristics |
293T cells
|
| Treatment protocol |
Sample 1x-A is from the sample New-A which is rehybridized after once-stripped. Sample 1x-B is from the sample New-B which is rehybridized after once-stripped. Sample 2x-B and 3x-B is from New-B which is rehybridized after twice-, and triple-stripped subsequently.
|
| Growth protocol |
Cells are grown in DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol® reagent (Invitrogen) was used to extract total RNA from 293T cells
|
| Label |
5'-DY547
|
| Label protocol |
Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
|
| |
|
| Channel 2 |
| Source name |
reference DNA oligonucleotides
|
| Organism |
synthetic construct |
| Characteristics |
reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs
|
| Treatment protocol |
Sample 1x-A is from the sample New-A which is rehybridized after once-stripped. Sample 1x-B is from the sample New-B which is rehybridized after once-stripped. Sample 2x-B and 3x-B is from New-B which is rehybridized after twice-, and triple-stripped subsequently.
|
| Growth protocol |
Cells are grown in DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Trizol® reagent (Invitrogen) was used to extract total RNA from 293T cells
|
| Label |
Alexa Fluor® 647
|
| Label protocol |
Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’. Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.
|
| |
|
| |
| Hybridization protocol |
A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA). Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.
|
| Scan protocol |
Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).
|
| Description |
293T New B
|
| Data processing |
BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities. GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.
|
| |
|
| Submission date |
Jan 29, 2008 |
| Last update date |
May 30, 2008 |
| Contact name |
Xiaoxiao Zhang |
| E-mail(s) |
zhang688@umn.edu
|
| Organization name |
University of Minnesota
|
| Street address |
312 Church St. SE
|
| City |
Minneapolis |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL6432 |
| Series (1) |
| GSE10305 |
A method of stripping custom microarrays |
|
