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Sample GSM1701116 Query DataSets for GSM1701116
Status Public on Oct 28, 2015
Title Gp2 pos2
Sample type RNA
 
Source name Mouse mTECs
Organism Mus musculus
Characteristics tra specificity: Gp2 positive mTECs
cell type: FACS isolated medullary thymic epithelial cells
Extracted molecule total RNA
Extraction protocol Total RNA of primary sorted mTECs was isolated and purified using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturers` protocol. Quality control was performed using Agilent Bioanalyser.
Label biotin
Label protocol Biotin-labeled cRNA for hybridization was prepared according to Illumina`s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992). In brief, 200 ng total RNA was used for cDNA synthesis, followed by an in vitro transcription step for amplification and labeling to synthesize biotin-labelled cRNA using the MessageAmp II RNA amplification kit (Ambion) and biotin-16-UTP (Roche).
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated.
Description biological replicate to sample 10
Sample 11
Data processing The data were normalised using quantile normalisation in R
 
Submission date Jun 01, 2015
Last update date Oct 28, 2015
Contact name Kristin Rattay
E-mail(s) [email protected]
Organization name German Cancer Research Center
Department D090
Lab Developmental Immunology
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL17543
Series (1)
GSE69435 Genome-wide analysis of TRA (tissue restricted antigen)-specific co-expression groups in mouse medullary thymic epithelial cells (mTECs)

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 122.4924455 0.002487005
ILMN_1251402 99.00077345 0.625279604
ILMN_3122480 102.5654838 0.359350038
ILMN_1230863 91.5222636 0.998356276
ILMN_2599935 192.182184 4.07E-07
ILMN_1249762 117.7208506 0.003774047
ILMN_2653194 102.0115854 0.342094954
ILMN_1227991 92.94105468 0.987331278
ILMN_2445236 103.7454714 0.296739336
ILMN_2675543 110.3431201 0.068822259
ILMN_2635314 100.641452 0.47577562
ILMN_1212991 134.3878968 1.50E-05
ILMN_2686883 102.4885909 0.364373122
ILMN_1223534 91.30880818 0.996532187
ILMN_2514305 168.5382485 2.71E-07
ILMN_2751818 112.0441594 0.067736537
ILMN_1217583 109.7783808 0.044039376
ILMN_1222597 104.8963007 0.13018413
ILMN_1242561 105.3012647 0.175771736
ILMN_2728634 109.9990307 0.028608081

Total number of rows: 46089

Table truncated, full table size 1617 Kbytes.




Supplementary file Size Download File type/resource
GSM1701116_9249051097_F_Grn.idat.gz 2.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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