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Detailed information about clone names, coordinates and accession numbers have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Platform accession number GPL5681.
The details of the EDMA platform array have been deposited in NCBI's Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO, Platform accession number: GPL18384.
The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (GEO) [ 24, 25] and are accessible through GEO Platform accession number GPL6413 and Series accession number GSE25511 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE25511).nih.gov/geo/query/acc.cgi acc=GSE25511
The Affymetrix raw data was downloaded from NCBI GEO (platform accession number is GPL2025; series accession number is GSE7256) [28].
The Affymetrix raw data for 983 arrays made with japonica and indica samples were downloaded from NCBI GEO (platform Accession Number is GPL2025) (Additional file 1: Table S1).
For microarray analysis of rice NCX genes, Affymetrix GeneChip rice genome arrays (http://www.ncbi.nlm.nih.gov/geo/; Gene Expression Omnibus platform accession nos. GSE6893) was used.
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In addition, GEO platform GPL16290 accession number (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GPL16290) contains all other files (probeset annotations, Affymetrix CDF, and Affymetrix 1lq) necessary to process CEL files generated from Tobacco Exon Array experiments.
A total of 11,019,886 (male) and 21,643,293 (female) read pairs of length 54 b were produced on the Illumina GAIIx platform (ArrayExpress accession number E-MTAB-714; ENA study accession number ERP000758).
The default endogenous control for the array platform (MammU6, Accession Number NR_004394, supplied in quadruplicate wells on the array) exhibited lower abundance in HIV/MDD pooled sample.
The array design is deposited in the GEO platform under accession number GPL9193.
We used a cDNA microarray NCBI GEO database (Platform GPL13527, accession number GSE30287) [ 46].
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