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Sample GSM4951210 Query DataSets for GSM4951210
Status Public on Jun 30, 2021
Title Varadan_Seedlings-Root_100
Sample type RNA
 
Source name root
Organism Oryza sativa
Characteristics variety: Varadan
developmental stage: 14 days seedling
treatment: Supplemented nitrogen
tissue: root
Growth protocol Hydroponics 14 days old seedling root
Extracted molecule total RNA
Extraction protocol The seeds of two varieties viz, Prasanna amd Varadan were washed with sodium hypochlorite followed by five washes of one min each. The seeds were kept in petri plates lined with moistened filter paper for germination. After seven days the seedlings were transferred to Yoshida medium with nitrogen for 10 days. Then the seedlings were transferred in Yoshida media with supplemented N and without N to observed the response of genotypes under N supplementation and without N supplementation. Total RNA was isolated from roots in replication
Label biotin
Label protocol Standard Affymetrix protocol
 
Hybridization protocol Amount of signal from the 3’ probe set to either the mid or 5’ probe sets, a measure of the quality of the RNA hybridized to the chip
Scan protocol Standard Affymetrix protocol
.CEL files obtained for each sample were processed through MAS 5 algorithm
Description NMA15
Data processing Present/Marginal/Absent calls were generated for each probe-set, using MAS 5.0 algorithm recommended by Affymetrix. % Present calls should be studied for each sample and if they are greater than 40%, the sample is considered as qualified for the downstream analysis.
 
Submission date Dec 01, 2020
Last update date Jun 30, 2021
Contact name C N Neeraja
E-mail(s) cnneeraja@gmail.com
Organization name ICAR-Indian Institute of Rice Research
Department Crop improvement
Lab Biotechnology
Street address Principal Scientist, ICAR-IIRR, Rajendranagar, Hyderabad 500030
City Hyderabad
State/province Telangana
ZIP/Postal code 500030
Country India
 
Platform ID GPL2025
Series (1)
GSE162412 Differential expression of genes in roots of rice seedlings with contrasting response under low nitrogen

Data table header descriptions
ID_REF
VALUE MAS 5

Data table
ID_REF VALUE
AFFX-BioB-3_at 1052.906382
AFFX-BioB-5_at 1032.895602
AFFX-BioB-M_at 1576.422575
AFFX-BioC-3_at 4257.34031
AFFX-BioC-5_at 3946.981491
AFFX-BioDn-3_at 14031.69183
AFFX-BioDn-5_at 7604.259309
AFFX-CreX-3_at 80310.8997
AFFX-CreX-5_at 69947.80878
AFFX-DapX-3_at 17534.26717
AFFX-DapX-5_at 1631.664613
AFFX-DapX-M_at 7833.753743
AFFX-LysX-3_at 2603.114299
AFFX-LysX-5_at 653.5360128
AFFX-LysX-M_at 1129.89178
AFFX-Mgr-actin-3_at 111.7443792
AFFX-Mgr-actin-5_at 14.87702551
AFFX-Mgr-actin-M_at 10.92284463
AFFX-Mgr-ef1a-3_at 723.7778528
AFFX-Mgr-ef1a-3_x_at 347.9047337

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.




Supplementary file Size Download File type/resource
GSM4951210_ZZ231332.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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