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Sample GSM764337 Query DataSets for GSM764337
Status Public on Nov 30, 2012
Title Meis-nega_TEC_rep1
Sample type RNA
 
Source name Meis-negative
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Meis1-EGFP BAC-transgenic [Tg(Meis1-EGFP)FO156Gsat/Mmcd]
age: 4 weeks
meis1 expression levels: Negative
cell type: CD45- EpCAM+ thymic epithelial cell (TEC)
Extracted molecule total RNA
Extraction protocol Three populations of CD45- EpCAM+ thymic epithelial cells with different EGFP expression levels and cell sizes (EGFPhigh FSClow, EGFPint FSChigh and EGFP- FSClow) was sorted with a FACSAreaTMII (BD Bioscience, San Diego, CA) from 4-week-old Meis1-EGFP BAC-transgenic reporter mice, Tg(Meis1-EGFP)FO156Gsat/Mmcd), that were generated by the GENSAT BAC transgenic project. RNA was isolated using the Qiagen RNeasy micro kit (Qiagen) following the manufacturer's recommendations. The protocol includes differential lysis of cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cDNA was prepared from 10ng RNA using the WT-Ovation™ Pico RNA Amplification System (NuGEN) and Genomic Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 3 ug of Cy3 labeled cDNA (specific activity >15.0 pmol Cy3/ug cDNA) was hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description gene expression in mouse thymic epithelial cells lacking Meis1 expression
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol: GE1-v5_95_Feb07 and Grid: 014868_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data were analyzed using GeneSpring GX version 11.0.2 software (Agilent Technologies, Santa Clara, CA). Threshold raw signals to 1.0, Normalization algorithm: Percentile Shift, Normalization: Shift to 50 percentile
 
Submission date Jul 20, 2011
Last update date Nov 30, 2012
Contact name Ryo Goitsuka
E-mail(s) [email protected]
Phone +81-4-7121-4102
Fax +81-4-7121-4103
Organization name Research Institute for Biological Sciences
Department Division of Development & Aging
Lab Goitsuka Laboratory
Street address 2669 Yamazaki
City Noda-shi
State/province Chiba
ZIP/Postal code 279-0022
Country Japan
 
Platform ID GPL7202
Series (2)
GSE30825 Transcriptional signatures of thymic epithelial cells with distinct Meis1 expression levels
GSE30826 The role of Meis1 in the maintenance of postnatal thymic epithelial cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 0.035511494
DarkCorner 0.426239
A_52_P616356 -0.7185912
A_52_P580582 -3.176823
A_52_P403405 -1.5654297
A_52_P819156 0.15435266
A_51_P331831 -0.05464697
A_51_P430630 -0.262887
A_52_P502357 0.37383842
A_52_P299964 0.3245263
A_51_P356389 1.3496661
A_52_P684402 -0.13876915
A_51_P414208 -0.76281834
A_51_P280918 -0.89697385
A_52_P613688 3.4185345
A_52_P258194 -1.7256167
A_52_P229271 0.42371297
A_52_P214630 -2.9109268
A_52_P579519 0.28874302
A_52_P979997 0.40026808

Total number of rows: 41252

Table truncated, full table size 960 Kbytes.




Supplementary file Size Download File type/resource
GSM764337.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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