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Sample GSM3463678 Query DataSets for GSM3463678
Status Public on Jul 23, 2019
Title 8353_CP6105707: Notch1+ cells P7.1
Sample type RNA
 
Source name Notch1 positive cells isolated from developing retinas
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: retina
developmental stage: Postnatal Day 7 (P7)
cell type: Notch1 positive cells
Extracted molecule total RNA
Extraction protocol To isolate Notch1+ cells and Glast+ cells, we employed an immunomagnetic cell separation approach using monoclonal biotin-conjugated anti-Notch1 and anti-Glast mouse antibodies and anti-biotin magnetic microbeads. RNA was extracted from cells using the Absolutely RNA Nanoprep kit (Agilent Technologies, Santa Clara, CA).
Label Streptavidin-Alexa-647
Label protocol Biotin-labeled complementary RNA was made from the total RNA according to Van Gelder’s protocol (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.)
 
Hybridization protocol Biotinylated complementary RNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarray slides enclosed in custom hybridization chambers (for more information on the MEEBO oligonucleotide set please refer to http://alizadehlab.stanford.edu/). The slides were hybridized for 16-18 hours in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).
Scan protocol After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).
Description We processed individual samples that each contained 200,000-500,000 cells.
Data processing Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. The spot intensities were then normalized. After removing data for low quality spots, the mouse probes’ intensities were filtered to identify all probes with an intensity above a normalized threshold. For statistical analysis, microarray data were examined for differences by One-way ANOVA. Values of F > Fcrit. = 2.83 were designated as statistically significant.
 
Submission date Nov 08, 2018
Last update date Jul 25, 2019
Contact name Dmitry Ivanov
E-mail(s) divanov@med.miami.edu
Phone 305-482-4230
Organization name University of Miami Miller School of Medicine
Department Ophthalmology
Street address 1638 NW 10th Avenue
City Miami
State/province FL
ZIP/Postal code 33136
Country USA
 
Platform ID GPL25621
Series (2)
GSE122301 Gene expression profiling of developing murine Müller glia
GSE122337 Development and epigenetic plasticity of murine Müller glia

Data table header descriptions
ID_REF
VALUE untransform normalized signal intensity

Data table
ID_REF VALUE
1462 0.326623331
4702 27.10973647
7942 10.45194659
11182 205.1194519
14422 1.959739986
17662 7.512336613
20902 0.326623331
24142 3.26623331
27382 58.79219958
30622 38.21492973
33862 0.326623331
37102 725.7570415
1463 21.55713985
4703 6.53246662
7943 0.326623331
11183 0.326623331
14423 3.26623331
17663 1253.580344
20903 4.899349965
24143 4.572726634

Total number of rows: 34288

Table truncated, full table size 590 Kbytes.




Supplementary file Size Download File type/resource
GSM3463678_19748353.txt.gz 861.1 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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