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Sample GSM1954181 Query DataSets for GSM1954181
Status Public on Dec 01, 2016
Title adrenal cortex-at slaughter 143
Sample type RNA
 
Source name adrenal cortex
Organism Bos taurus
Characteristics gender: female
age at slaughter in days: 1187
year-season of slaughter: Spring2007
tissue: adrenal cortex
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the adrenal cortex of 147 animals using TRI Reagent (Sigma, Taufkirchen, Germany). After DNaseI treatment the RNA was further purified with the RNeasy Kit (QIAGEN, Hilden, Germany) following the manufacturers recommendations. RNA was quantified using the NanoDrop ND-1000 spectrophotometer (Peqlab, Erlangen, Germany). Integrity of RNA was checked by running 1 μg of RNA on a 1% agarose gel. Absence of DNA contamination was verified by PCR amplifying fragments of GAPDH with RNA as a template.
Label biotin
Label protocol 5.5 µg of cDNA was fragmented and labeled using the Affymetrix Terminal Labeling Kit and Affymetrix standard protocols
 
Hybridization protocol The fragmented cDNA was hybridized to the microarray using the Affymetrix Hyb-WashStain Kit and Affymetrix standard protocols
Scan protocol GeneChips were scanned using the GeneChip scanner 3000 (Affymetrix, St. Clara, USA)
Data processing Gene-level analysis and RMA normalization was performed using Affymetrix Expression Console software based on 147 Microarrays. Filtering of Probesets was performed using the detection above background algorithm. Probe sets that were present in 75% of all samples and transcripts with at least 50% of all probe sets present were included in the final analyses. Two samples (30 and 89) were excluded due to misssing phenotypic data.
BovGene-1_0-v1.pgf
BovGene-1_0-v1.mps
 
Submission date Nov 24, 2015
Last update date Dec 01, 2016
Contact name Bodo Brand
E-mail(s) brand@fbn-dummerstorf.de
Organization name Leibniz Institute of Farm Animal Biology
Street address Wilhelm-Stahl-Allee 2
City Dummerstorf
ZIP/Postal code 18196
Country Germany
 
Platform ID GPL16500
Series (1)
GSE75371 Adrenal cortex expression data of a German Holstein X Charolaise cross

Data table header descriptions
ID_REF
VALUE RMA normalized gene level expression values from Affymetrix Expression Console software for the 145 samples included in the study after filtering

Data table
ID_REF VALUE
12755617 14.47034
12755619 14.47034
12755612 14.27878
12842687 13.80099
12915609 13.92421
12910843 13.93627
12811304 13.76858
12903008 13.53825
12839924 13.50689
12718044 13.64085
12815289 13.60219
12910835 13.66372
12704189 13.36709
12910833 13.71939
12768107 13.39112
12910831 13.63473
12742026 13.3018
12875788 13.28028
12910851 13.54266
12863939 13.17501

Total number of rows: 10986

Table truncated, full table size 191 Kbytes.




Supplementary file Size Download File type/resource
GSM1954181_Segfam_NNR_WT_143.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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