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Sample GSM1944022 Query DataSets for GSM1944022
Status Public on Oct 31, 2016
Title CR21_532
Sample type RNA
 
Source name Total RNAs of Man-Su_30minutes
Organism Brassica rapa subsp. pekinensis
Characteristics genotype: Man-Su
treatment: cold stress 30 min
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description expression analysis of chinese cabbage (B.rapa ssp. pekinensis), Man-Su : cold stress conditions 30 minutes
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Nov 18, 2015
Last update date Oct 31, 2016
Contact name Chang-Kug Kim
E-mail(s) chang@korea.kr
Organization name National Institute of Agricultural Sciences (NAS)
Department Genomics Division
Street address 370, Nongsaengmyeong-ro
City Jeonju
ZIP/Postal code 54874
Country South Korea
 
Platform ID GPL17248
Series (1)
GSE75145 Expression analysis of chinese cabbage (B.rapa ssp. pekinensis) : cold stress conditions

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
Brapa_ESTC000001 8737.27
Brapa_ESTC000002 22812.19
Brapa_ESTC000003 6268.06
Brapa_ESTC000004 1236.74
Brapa_ESTC000005 21628.77
Brapa_ESTC000006 32126.90
Brapa_ESTC000007 249.14
Brapa_ESTC000008 7784.29
Brapa_ESTC000009 2749.97
Brapa_ESTC000010 13480.66
Brapa_ESTC000011 3479.57
Brapa_ESTC000012 4176.84
Brapa_ESTC000013 6635.04
Brapa_ESTC000014 3709.95
Brapa_ESTC000015 38841.89
Brapa_ESTC000016 8645.52
Brapa_ESTC000017 15291.24
Brapa_ESTC000018 29504.52
Brapa_ESTC000019 1087.89
Brapa_ESTC000020 30457.99

Total number of rows: 47554

Table truncated, full table size 1161 Kbytes.




Supplementary file Size Download File type/resource
GSM1944022_CR21_532.probe.gz 5.3 Mb (ftp)(http) PROBE
GSM1944022_CR21_532_nm_RMA.calls.gz 508.4 Kb (ftp)(http) CALLS
GSM1944022_CR21_532_nm_norm_RMA.pair.gz 5.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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