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Platform GPL10948 Query DataSets for GPL10948
Status Public on Oct 01, 2010
Title [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF (ATH1-121501.TAIR8)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Affymetrix
Manufacture protocol See manufacturer's web site.
 
Description The custom CDF was built by uniquely mapping 232,697 probe sequences to 21,389 Arabidopsis (TAIR8) gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>99% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).
 
Submission date Sep 20, 2010
Last update date Oct 01, 2010
Contact name Andy Pereira
E-mail(s) pereiraa@vbi.vt.edu
Phone 540-231-3784
Organization name Virginia Tech
Department Virginia Bioinformatics Institute
Lab Plant Stress Systems Biology
Street address Washington Street MC0477
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
 
Samples (12) GSM596123, GSM596124, GSM596125, GSM596126, GSM596127, GSM596128 
Series (1)
GSE24177 Gene expression changes in response to drought stress in Arabidopsis reveal early responses leading to acclimation in plant growth
Relations
Alternative to GPL198 (Alternative CDF [official])

Data table header descriptions
ID
ORF Locus tag
TAIR_ID The Arabidopsis Information Resource (TAIR) locus
Description Gene description
SPOT_ID

Data table
ID ORF TAIR_ID Description SPOT_ID
AT1G01010_at AT1G01010 AT1G01010 ANAC001 (Arabidopsis NAC domain containing protein 1); transcription factor
AT1G01030_at AT1G01030 AT1G01030 NGA3 (NGATHA3); transcription factor
AT1G01040_at AT1G01040 AT1G01040 DCL1 (DICER-LIKE1); ATP-dependent helicase/ ribonuclease III
AT1G01050_at AT1G01050 AT1G01050 ATPPA1 (ARABIDOPSIS THALIANA PYROPHOSPHORYLASE 1); inorganic diphosphatase/ pyrophosphatase
AT1G01060_at AT1G01060 AT1G01060 LHY (LATE ELONGATED HYPOCOTYL); DNA binding / transcription factor
AT1G01070_at AT1G01070 AT1G01070 nodulin MtN21 family protein
AT1G01080_at AT1G01080 AT1G01080 33 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putative
AT1G01090_at AT1G01090 AT1G01090 PDH-E1 ALPHA (PYRUVATE DEHYDROGENASE E1 ALPHA); pyruvate dehydrogenase (acetyl-transferring)
AT1G01100_at AT1G01100 AT1G01100 60S acidic ribosomal protein P1 (RPP1A)
AT1G01110_at AT1G01110 AT1G01110 IQD18 (IQ-domain 18)
AT1G01120_at AT1G01120 AT1G01120 KCS1 (3-KETOACYL-COA SYNTHASE 1); acyltransferase
AT1G01130_at AT1G01130 AT1G01130
AT1G01140_at AT1G01140 AT1G01140 CIPK9 (CBL-INTERACTING PROTEIN KINASE 9); kinase
AT1G01150_at AT1G01150 AT1G01150 DNA binding / zinc ion binding
AT1G01160_at AT1G01160 AT1G01160 GIF2 (GRF1-INTERACTING FACTOR 2)
AT1G01170_at AT1G01170 AT1G01170 ozone-responsive stress-related protein, putative
AT1G01180_at AT1G01180 AT1G01180
AT1G01190_at AT1G01190 AT1G01190 CYP78A8 (cytochrome P450, family 78, subfamily A, polypeptide 8); oxygen binding
AT1G01200_at AT1G01200 AT1G01200 AtRABA3 (Arabidopsis Rab GTPase homolog A3); GTP binding
AT1G01220_at AT1G01220 AT1G01220 GHMP kinase-related

Total number of rows: 21517

Table truncated, full table size 1538 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL10948_ATH1-121501.TAIR8.custom.CDF.gz 6.4 Mb (ftp)(http) CDF

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