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Platform GPL1074 Query DataSets for GPL1074
Status Public on Mar 19, 2004
Title GNF1H
Technology type in situ oligonucleotide
Distribution non-commercial
Organism Homo sapiens
 
Description GNF1H
In 2002, we identified a non-redundant set of human target sequences using the following sources: RefSeq (15,491 sequences), Celera (49,859 sequences), and Ensembl (33,698 sequences). First, all sequences were RepeatMasked to remove repetitive elements. Next, sequence identity between individual sequences was established using pairwise BLAT or BLAST and sim4. The results from single-linkage clustering were further triaged to produce a final target set of 44,775 targets with the highest degree of confidence of computational prediction (biasing toward sequences containing Interpro domains and away from non-coding RNAs). Finally, the human sequence set was pruned of all targets already represented on Affymetrix's commercially available U133A array, leaving 22,645 target sequences for our custom array. The final target sets were submitted to the Affymetrix's chip design pipeline for fabrication of the GNF1H arrays.

Update: At the time of publication (2004, DOI: 10.1073/pnas.0400782101), by request from Celera, we have masked any and all sequences that were derived from Celera data. We have been able to re-annotate and associate 11,406 probe sets to public data, and for the rest (11,086 probe sets), we masked the sequences by poly-N and replaced their annotation if any with "predicted transcript (Celera)" and their target regions and individual probe sequences are all unavailable. For approximately 750 more probe sets, the annotation is based on the orthologous annotation data available in 2004 and the phrase "a predicted transcript (Celera), similar to :[insert the rest [e.g. M.musculus]]" should be implied. Caveat emptor: Even though all these sets are designed from human transcripts and computational predictions, it should not be expected that they are efficient to assay the modern version of any human transcript. All individual probe sequences for 11,406 sets are provided for the interested parties to do their own sequence analysis (suggested route: blast/blat or otherwise align individual probes to the most recent genome+transcriptome database and use a >8 out of 11 voting system to determine the most likely target(s)). Such analysis will be in most cases more precise than any precomputed annotation (however, in many cases this new, precise annotation will be "intergenic region", "intron", "antisense to :" - due to old age of the array probes may have been designed outside of the true UTR, the 2002 genomic sequence may have been misassembled, predictions were truncated or completely wrong etc).
 
Submission date Mar 18, 2004
Last update date Sep 22, 2011
Contact name John R Walker
E-mail jwalker@gnf.org
Phone 858-812-1636
Organization name Genomics Institute of the Novartis Research Foundation
Lab Genetics Core
Street address 10675 John Jay Hopkins
City San Diego
State/province CA
ZIP/Postal code 92121
Country USA
 
Samples (158) GSM18706, GSM18707, GSM18708, GSM18709, GSM18710, GSM18711 
Series (1)
GSE1133 tissue-specific pattern of mRNA expression

Data table header descriptions
ID Probe Set Name
Identifier_Source
Description
Sequence_Type
SPOT_ID Column added by GEO staff to facilitate sequence tracking in Entrez GEO
SEQUENCE

Data table
ID Identifier_Source Description Sequence_Type SPOT_ID SEQUENCE
200000_s_at GNF gb:NM_006445.1 /DEF=Homo sapiens U5 snRNP-specific protein (220 kD), ortholog of S. cerevisiae Prp8p (PRP8), mRNA. /FEA=mRNA /GEN=PRP8 /PROD=U5 snRNP-specific protein (220 kD), ortholog ofS. cerevisiae Prp8p /DB_XREF=gi:5453983 /UG=Hs.181368 U5 snRNP-specific protein (220 kD), ortholog of S. cerevisiae Prp8p /FL=gb:AB007510.1 gb:AF092565.1 gb:NM_006445.1 mRNA 200000_s_at
200001_at GNF gb:NM_001749.1 /DEF=Homo sapiens calpain 4, small subunit (30K) (CAPN4), mRNA. /FEA=mRNA /GEN=CAPN4 /PROD=calpain 4 small subunit /DB_XREF=gi:4502564 /UG=Hs.74451 calpain 4, small subunit (30K) /FL=gb:BC000592.1 gb:NM_001749.1 mRNA 200001_at
200002_at GNF gb:NM_007209.1 /DEF=Homo sapiens ribosomal protein L35 (RPL35), mRNA. /FEA=mRNA /GEN=RPL35 /PROD=ribosomal protein L35 /DB_XREF=gi:6005859 /UG=Hs.182825 ribosomal protein L35 /FL=gb:BC000348.1 gb:U12465.1 gb:NM_007209.1 mRNA 200002_at
200003_s_at GNF gb:NM_000991.1 /DEF=Homo sapiens ribosomal protein L28 (RPL28), mRNA. /FEA=mRNA /GEN=RPL28 /PROD=ribosomal protein L28 /DB_XREF=gi:4506626 /UG=Hs.4437 ribosomal protein L28 /FL=gb:BC000072.1 gb:NM_000991.1 gb:U14969.1 mRNA 200003_s_at
200004_at GNF gb:NM_001418.1 /DEF=Homo sapiens eukaryotic translation initiation factor 4 gamma, 2 (EIF4G2), mRNA. /FEA=mRNA /GEN=EIF4G2 /PROD=eukaryotic translation initiation factor 4gamma, 2 /DB_XREF=gi:4503538 /UG=Hs.183684 eukaryotic translation initiation factor 4 gamma, 2 /FL=gb:U73824.1 gb:U76111.1 gb:NM_001418.1 mRNA 200004_at
200005_at GNF gb:NM_003753.1 /DEF=Homo sapiens eukaryotic translation initiation factor 3, subunit 7 (zeta, 6667kD) (EIF3S7), mRNA. /FEA=mRNA /GEN=EIF3S7 /PROD=eukaryotic translation initiation factor 3,subunit 7 (zeta, 6667kD) /DB_XREF=gi:4503522 /UG=Hs.55682 eukaryotic translation initiation factor 3, subunit 7 (zeta, 6667kD) /FL=gb:BC000328.1 gb:BC000469.1 gb:U54558.1 gb:NM_003753.1 mRNA 200005_at
200006_at GNF gb:NM_007262.1 /DEF=Homo sapiens RNA-binding protein regulatory subunit (DJ-1), mRNA. /FEA=mRNA /GEN=DJ-1 /PROD=RNA-binding protein regulatory subunit /DB_XREF=gi:6005748 /UG=Hs.10958 RNA-binding protein regulatory subunit /FL=gb:AF021819.1 gb:NM_007262.1 gb:D61380.1 mRNA 200006_at
200007_at GNF gb:NM_003134.1 /DEF=Homo sapiens signal recognition particle 14kD (homologous Alu RNA-binding protein) (SRP14), mRNA. /FEA=mRNA /GEN=SRP14 /PROD=signal recognition particle 14kD (homologous AluRNA-binding protein) /DB_XREF=gi:4507210 /UG=Hs.180394 signal recognition particle 14kD (homologous Alu RNA-binding protein) /FL=gb:NM_003134.1 gb:U07857.1 mRNA 200007_at
200008_s_at GNF gb:D13988.1 /DEF=Human rab GDI mRNA, complete cds. /FEA=mRNA /PROD=human rab GDI /DB_XREF=gi:285974 /UG=Hs.56845 GDP dissociation inhibitor 2 /FL=gb:BC005145.1 gb:D13988.1 gb:NM_001494.2 mRNA 200008_s_at
200009_at GNF gb:NM_001494.2 /DEF=Homo sapiens GDP dissociation inhibitor 2 (GDI2), mRNA. /FEA=mRNA /GEN=GDI2 /PROD=GDP dissociation inhibitor 2 /DB_XREF=gi:6598322 /UG=Hs.56845 GDP dissociation inhibitor 2 /FL=gb:BC005145.1 gb:D13988.1 gb:NM_001494.2 mRNA 200009_at
200010_at GNF gb:NM_000975.1 /DEF=Homo sapiens ribosomal protein L11 (RPL11), mRNA. /FEA=mRNA /GEN=RPL11 /PROD=ribosomal protein L11 /DB_XREF=gi:4506594 /UG=Hs.179943 ribosomal protein L11 /FL=gb:L05092.1 gb:NM_000975.1 mRNA 200010_at
200011_s_at GNF gb:NM_001659.1 /DEF=Homo sapiens ADP-ribosylation factor 3 (ARF3), mRNA. /FEA=mRNA /GEN=ARF3 /PROD=ADP-ribosylation factor 3 /DB_XREF=gi:4502202 /UG=Hs.119177 ADP-ribosylation factor 3 /FL=gb:M74491.1 gb:NM_001659.1 mRNA 200011_s_at
200012_x_at GNF gb:NM_000982.1 /DEF=Homo sapiens ribosomal protein L21 (gene or pseudogene) (RPL21), mRNA. /FEA=mRNA /GEN=RPL21 /PROD=ribosomal protein L21 (gene or pseudogene) /DB_XREF=gi:4506610 /UG=Hs.184108 ribosomal protein L21 /FL=gb:BC001603.1 gb:NM_000982.1 gb:U14967.1 gb:U25789.1 mRNA 200012_x_at
200013_at GNF gb:NM_000986.1 /DEF=Homo sapiens ribosomal protein L24 (RPL24), mRNA. /FEA=mRNA /GEN=RPL24 /PROD=ribosomal protein L24 /DB_XREF=gi:4506618 /UG=Hs.184582 ribosomal protein L24 /FL=gb:BC000690.1 gb:M94314.1 gb:NM_000986.1 mRNA 200013_at
200014_s_at GNF gb:NM_004500.1 /DEF=Homo sapiens heterogeneous nuclear ribonucleoprotein C (C1C2) (HNRPC), mRNA. /FEA=mRNA /GEN=HNRPC /PROD=heterogeneous nuclear ribonucleoprotein C(C1C2) /DB_XREF=gi:4758543 /UG=Hs.182447 heterogeneous nuclear ribonucleoprotein C (C1C2) /FL=gb:BC003394.1 gb:M16342.1 gb:NM_004500.1 mRNA 200014_s_at
200015_s_at GNF gb:NM_004404.1 /DEF=Homo sapiens neural precursor cell expressed, developmentally down-regulated 5 (NEDD5), mRNA. /FEA=mRNA /GEN=NEDD5 /PROD=neural precursor cell expressed, developmentallydown-regulated 5 /DB_XREF=gi:4758157 /UG=Hs.155595 neural precursor cell expressed, developmentally down-regulated 5 /FL=gb:D28540.1 gb:NM_004404.1 gb:D63878.1 mRNA 200015_s_at
200016_x_at GNF gb:NM_002136.1 /DEF=Homo sapiens heterogeneous nuclear ribonucleoprotein A1 (HNRPA1), mRNA. /FEA=mRNA /GEN=HNRPA1 /PROD=heterogeneous nuclear ribonucleoprotein A1 /DB_XREF=gi:4504444 /UG=Hs.249495 heterogeneous nuclear ribonucleoprotein A1 /FL=gb:NM_002136.1 mRNA 200016_x_at
200017_at GNF gb:NM_002954.1 /DEF=Homo sapiens ribosomal protein S27a (RPS27A), mRNA. /FEA=mRNA /GEN=RPS27A /PROD=ribosomal protein S27a /DB_XREF=gi:4506712 /UG=Hs.3297 ribosomal protein S27a /FL=gb:BC001392.1 gb:BC005328.1 gb:NM_002954.1 mRNA 200017_at
200018_at GNF gb:NM_001017.1 /DEF=Homo sapiens ribosomal protein S13 (RPS13), mRNA. /FEA=mRNA /GEN=RPS13 /PROD=ribosomal protein S13 /DB_XREF=gi:4506684 /UG=Hs.165590 ribosomal protein S13 /FL=gb:BC000475.1 gb:L01124.1 gb:NM_001017.1 mRNA 200018_at
200019_s_at GNF gb:NM_001997.1 /DEF=Homo sapiens Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 (FAU), mRNA. /FEA=mRNA /GEN=FAU /PROD=Finkel-Biskis-Reilly murine sarcoma virus(FBR-MuSV) ubiquitously expressed (fox derived); ribosomalprotein S30 /DB_XREF=gi:4503658 /UG=Hs.177415 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 /FL=gb:NM_001997.1 mRNA 200019_s_at

Total number of rows: 22639

Table truncated, full table size 6463 Kbytes.






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Supplementary file Size Download File type/resource
GPL1074.CDF.gz 6.8 Mb (ftp)(http) CDF
GPL1074.CIF.gz 1.4 Kb (ftp)(http) CIF
GPL1074.GIN.gz 338.0 Kb (ftp)(http) GIN
GPL1074.PSI.gz 115.4 Kb (ftp)(http) PSI
GPL1074.SIF.gz 1.1 Mb (ftp)(http) SIF
GPL1074.probe.gz 3.3 Mb (ftp)(http) PROBE
GPL1074.tab.gz 3.2 Mb (ftp)(http) TAB
GPL1074_PRB.TXT.gz 3.2 Mb (ftp)(http) TXT

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