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Sample GSM599878 Query DataSets for GSM599878
Status Public on Oct 01, 2010
Title 3-cell, rep3
Sample type RNA
 
Source name Total RNA from 3 cells
Organism Mus musculus
Characteristics cell line: R1
cell type: mouse embryonic stem cells
Treatment protocol Drop-on-demand total RNA analysis steps: 1) Heterogeneous sample was collected, 2) cells were stained with antibody and patterned with cell-encapsulating droplets, 3) specific homogeneous samples containing target cells were produced by a cell droplet patterning platform; homogeneous samples were identified by an automated imaging system, 4) total RNA gene expression analysis with microarray.
Extracted molecule total RNA
Extraction protocol 100 µL of RLT Buffer solution (QIAGEN, 1% mercaptoethanol) was used to lyse the ejected cells and to preserve the RNA. Qiagen RNeasy Minikit (QIAGEN) was used to purify the total RNA.
Label Cy5
Label protocol 2-3 ng sample (total RNA) is primed with the T7 oligo (dT) primer to synthesize cDNA containing a T7 promoter sequence. Second-strand cDNA synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. In vitro transcription to synthesize cRNA generates multiple copies of biotinylated cRNA from the double-stranded cDNA templates.
 
Hybridization protocol 10 μg of labeled cRNA was fragmented, denatured at 90°C for 5 min, and then hybridized at 37°C for 20 hours using direct hybridization array kits (from AppliedMicroarrays CodeLink). The arrays were then washed in buffer at 47°C for 60 minutes. After washing, the arrays were incubated at room temperature for 30 minutes with a fluorophore (Streptavidin-Alexa Fluor 647, Invitrogen Eugene, OR), run through a series of 5 minute rinses, and spun dry.
Scan protocol Arrays were scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).
Description M1.C
Data processing Raw intensities were normalized by CodeLink software based on global median for each array. The gene expression measurements were further normalized to a median expression level of 1.0 across the arrays. 1000 genes with the highest expression levels “>1” in the experimental samples was used for comparisons.
 
Submission date Sep 23, 2010
Last update date Sep 25, 2010
Contact name Lingsheng Dong
Organization name Brigham and Women's Hospital
Department Renal Division
Street address 75 Francis Street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL8063
Series (1)
GSE24330 Drop-on-demand single cell isolation and total RNA analysis

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 0.894127137
2 3.768252844
3 0.861314936
4 0.790843644
5 1.211752024
6 2.988502122
7 0.873690358
8 2.606275219
9 0.394769346
10 1.551026644
11 2.116289213
12 1.084445459
13 0.613199739
14 1.336832557
15 0.856529926
16 1.849294091
17 2.156374761
18 1.957098646
19 0.947772586
20 0.851744916

Total number of rows: 36227

Table truncated, full table size 621 Kbytes.




Supplementary file Size Download File type/resource
GSM599878.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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