R/allEndpoints.R
get_gene_probes.RdRetrieve the probes associated to a genes across all platforms
An ensembl gene identifier which typically starts with ensg or an ncbi gene identifier or an official gene symbol approved by hgnc
The offset of the first retrieved result.
Defaults to 20. Limits the result to specified amount
of objects. Has a maximum value of 100. Use together with offset and
the totalElements attribute in the output to
compile all data if needed.
TRUE to receive results as-is from Gemma, or FALSE to enable
parsing. Raw results usually contain additional fields and flags that are
omitted in the parsed results.
Whether or not to save to cache for future calls with the
same inputs and use the result saved in cache if a result is already saved.
Doing options(gemma.memoised = TRUE) will ensure that the cache is always
used. Use forget_gemma_memoised to clear the cache.
The name of a file to save the results to, or NULL to not write
results to a file. If raw == TRUE, the output will be the raw endpoint from the
API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
Whether or not to overwrite if a file exists at the specified filename.
A data table with information about the probes representing a gene across
all platrofms. A list if raw = TRUE.
A 404 error if the given identifier does not map to any genes.
The fields of the output data.table are:
element.name: Name of the element. Typically the probeset name
element.description: A free text field providing optional information about the element
platform.shortName: Shortname of the platform given by Gemma. Typically the GPL identifier.
platform.name: Full name of the platform
platform.ID: Id number of the platform given by Gemma
platform.type: Type of the platform.
platform.description: Free text field describing the platform.
platform.troubled: Whether the platform is marked as troubled by a Gemma curator.
taxon.name: Name of the species platform was made for
taxon.scientific: Scientific name for the taxon
taxon.ID: Internal identifier given to the species by Gemma
taxon.NCBI: NCBI ID of the taxon
taxon.database.name: Underlying database used in Gemma for the taxon
taxon.database.ID: ID of the underyling database used in Gemma for the taxon
get_gene_probes(1859)
#> element.name
#> <char>
#> 1: 215234_at
#> 2: 211541_s_at
#> 3: 211079_s_at
#> 4: 209033_s_at
#> 5: 239308_at
#> 6: 215234_at
#> 7: 211541_s_at
#> 8: 211079_s_at
#> 9: 209033_s_at
#> 10: 827_s_at
#> 11: 36947_s_at
#> 12: 36946_at
#> 13: 33946_at
#> 14: 1512_at
#> 15: 543
#> 16: 75416_at
#> 17: 37562
#> 18: 37071
#> 19: 23356
#> 20: 5474
#> element.name
#> element.description
#> <char>
#> 1: MRNA, partial cDNA sequence from cDNA selection, DCR1-16.0,
#> 2: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 3: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A /// dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 4: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 5: Transcribed locus, strongly similar to XP_514894.1 PREDICTED: hypothetical protein XP_514894 [Pan troglodytes]
#> 6: MRNA, partial cDNA sequence from cDNA selection, DCR1-16.0,
#> 7: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 8: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A /// dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 9: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 10: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 11: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 12: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 13: MRNA, partial cDNA sequence from cDNA selection, DCR1-16.0,
#> 14: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 15: Multiple external sequence references: D86550,NM_001396,NM_101395,NM_130436,NM_130437,NM_130438;
#> 16: Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> 17: <NA>
#> 18: <NA>
#> 19: <NA>
#> 20: dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
#> element.description
#> platform.shortName
#> <char>
#> 1: GPL96
#> 2: GPL96
#> 3: GPL96
#> 4: GPL96
#> 5: GPL570
#> 6: GPL570
#> 7: GPL570
#> 8: GPL570
#> 9: GPL570
#> 10: GPL91
#> 11: GPL91
#> 12: GPL91
#> 13: GPL91
#> 14: GPL91
#> 15: GPL560
#> 16: GPL95
#> 17: GPL962
#> 18: GPL962
#> 19: GPL962
#> 20: GPL180
#> platform.shortName
#> platform.name
#> <char>
#> 1: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
#> 2: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
#> 3: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
#> 4: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A
#> 5: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
#> 6: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
#> 7: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
#> 8: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
#> 9: Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
#> 10: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A
#> 11: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A
#> 12: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A
#> 13: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A
#> 14: Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A
#> 15: Developmental Toxicity of the Mouse Embryo (DTME)
#> 16: Affymetrix GeneChip Human Genome U95 Set HG-U95E
#> 17: CHUGAI 41K
#> 18: CHUGAI 41K
#> 19: CHUGAI 41K
#> 20: SVC
#> platform.name
#> platform.ID platform.type
#> <int> <char>
#> 1: 1 ONECOLOR
#> 2: 1 ONECOLOR
#> 3: 1 ONECOLOR
#> 4: 1 ONECOLOR
#> 5: 4 ONECOLOR
#> 6: 4 ONECOLOR
#> 7: 4 ONECOLOR
#> 8: 4 ONECOLOR
#> 9: 4 ONECOLOR
#> 10: 8 ONECOLOR
#> 11: 8 ONECOLOR
#> 12: 8 ONECOLOR
#> 13: 8 ONECOLOR
#> 14: 8 ONECOLOR
#> 15: 13 TWOCOLOR
#> 16: 24 ONECOLOR
#> 17: 36 TWOCOLOR
#> 18: 36 TWOCOLOR
#> 19: 36 TWOCOLOR
#> 20: 40 TWOCOLOR
#> platform.ID platform.type
#> platform.description
#> <char>
#> 1: The U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002. The set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes. Sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation. Keywords = high density oligonucleotide array\nFrom GPL96\nLast Updated: Mar 09 2006
#> 2: The U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002. The set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes. Sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation. Keywords = high density oligonucleotide array\nFrom GPL96\nLast Updated: Mar 09 2006
#> 3: The U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002. The set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes. Sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation. Keywords = high density oligonucleotide array\nFrom GPL96\nLast Updated: Mar 09 2006
#> 4: The U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002. The set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes. Sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation. Keywords = high density oligonucleotide array\nFrom GPL96\nLast Updated: Mar 09 2006
#> 5: Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). \nFrom GPL570\nLast Updated: Mar 09 2006
#> 6: Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). \nFrom GPL570\nLast Updated: Mar 09 2006
#> 7: Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). \nFrom GPL570\nLast Updated: Mar 09 2006
#> 8: Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). \nFrom GPL570\nLast Updated: Mar 09 2006
#> 9: Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release). In addition, there are 9,921 new probe sets representing approximately 6,500 new genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). \nFrom GPL570\nLast Updated: Mar 09 2006
#> 10: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters. This platform can also be used to submit data for the HG_U95A [version 1] array. Keywords = high density oligonucleotide array\nFrom GPL91\nLast Updated: Mar 09 2006
#> 11: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters. This platform can also be used to submit data for the HG_U95A [version 1] array. Keywords = high density oligonucleotide array\nFrom GPL91\nLast Updated: Mar 09 2006
#> 12: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters. This platform can also be used to submit data for the HG_U95A [version 1] array. Keywords = high density oligonucleotide array\nFrom GPL91\nLast Updated: Mar 09 2006
#> 13: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters. This platform can also be used to submit data for the HG_U95A [version 1] array. Keywords = high density oligonucleotide array\nFrom GPL91\nLast Updated: Mar 09 2006
#> 14: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters. This platform can also be used to submit data for the HG_U95A [version 1] array. Keywords = high density oligonucleotide array\nFrom GPL91\nLast Updated: Mar 09 2006
#> 15: Developmental Toxicity of the Mouse Embryo (DTME) includes expression data from early embryos at risk for teratogen-induced eye malformations. Early mouse embryos were exposed to various teratogens during neurulation stages with the aim of correlating large-scale changes in gene expression with a generic histopathological biomarker (p53 protein induction) across the critical period during exposure, and with the risk of malformations in term fetuses (the various exposure scenarios produce ~10% risk of malformations in term fetuses averaged across 50 conditions of the experiment). Microarray analysis was performed on RNA from the embryo, prosencephalon, or headfold. Each condition for microarray analysis was replicated with independent sampling and reversal of labeling assignments (100 samples total). DTME compares genes expressed between test vs. reference samples as evidenced by data from two-channel MICROMAX system from PerkinElmer Life Sciences (Wellesley, MA 02481-4078, USA). It also includes a series of comparisons of early optic development in the optic primordium from mouse and rat embryos harvested at equivalent morphogenetic stages. The microarray platform uses a novel integrative chemistry that culminates massive signal amplification and greatly enhanced detection. The method incorporates unique two-channel indirect labeling of target RNA products with biotinyl-11-dCTP and fluorescein-12-dCTP (or dinitrophenol-11-dCTP) with post-hybridization amplification through conventional immunodetection and tyramide signal amplification. The probe was spotted with 2.4K sequence-verified human gene elements (single or duplicate) from 50 different cDNA libraries and positive- and negative- control genes. The cDNAs represent more than 10 different tissue sources: 80% brain-derived and more than 40% full-length cDNA sequences and a range of human diseases, metabolic, and regulatory pathways. The probe has been shown effective with target RNA from human, mouse, or rat biosources. The dataset includes "absolute" and "relative" values. Absolute values represent the background-corrected signal. For single-spot 2400 arrays this means one measurement for every spotted element and each color channel. Relative values represent ratiometric data normalized as follows: transformation to log2-space; lowess correction of MxA plot; internal standardization by mean absolute deviation; and normalization between replica pairs in each condition. Keywords = mouse Keywords = embryo Keywords = teratogen Keywords = toxicity Keywords = development Keywords = eye\nFrom GPL560\nLast Updated: May 26 2005
#> 16: The Human Genome U95 (HG-U95) Set, consisting of five GeneChip arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database (Build 95). Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent approximately 50,000 EST clusters. Keywords = high density oligonucleotide array\nFrom GPL95\nLast Updated: Jul 28 2006
#> 17: Patients and Sample Preparation. We analyzed NT samples from 38 patients undergoing surgery at the Cancer Institute Hospital, Tokyo, during May 1996 ? May 2001. All samples were collected with informed consent and ethical committee approval and were grossly dissected, snap-frozen in liquid nitrogen within 20 minutes of removal. Initial diagnosis of each sample from frozen section was later confirmed by detailed analysis of paraffin sections and immunohistochemistry. Following WHO guidelines,1 17 tumours were classified as SCLC including two combined SCLC with adenocarcinoma (SCLC-AD), 8 as LCNEC, including 2 combined LCNEC with AD (LCNEC-AD), 12 as TC and 1 as AC. The prevalence of LCNEC as a percentage all lung cancer resected at the Cancer Institute during the period was 2.7%. Since LCNEC is described as a variant of large cell carcinoma MAGE(LCC), we also analyzed thirteen LCC samples. Twelve well differentiated AD samples were included to aid interpretation of expression profiles for the SCLC-AD and LCNEC-AD samples, and to allow identification of markers that distinguish NT from non-small cell lung cancer. We included thirty normal lung samples from unrelated individuals. Finally 11 SCLC cell lines were incorporated into the analysis. Full clinical details of all tumour samples and cell lines are provided in supplementary table 1. Reference RNA, a mixture of lung cancer cell lines and normal lung, is exactly as described previously.5 Cell lines were obtained from the American Type Culture Collection. the Japanese Collection of Research Bioresources, or The RIKEN cell bank. cDNA microarray Each microarray contains 40,368 elements, of which 39,936 are derived from IMAGE cDNA clones purchased from Research Genetics (Huntsville, Alabama). This clone set was supplemented with 384 proprietary clones and 48 control elements. According to our latest estimate, the array represents 29,487 unique UNIGENE clusters accounting for 9,085 named genes, 15,276 ESTs and 5126 other un-named genes (for example, clones described as hypothetical proteins). Clones were purchased as sequence verified, but we estimate an error rate of at least 10%. Genes mentioned by name in this paper have been re-sequenced. cDNA PCR products were resuspended in 50% DMSO and printed at a pitch of 150 µm onto CMT-GAPS slides (Corning, Corning, NY) using a MicroGrid II spotting robot fitted with 10K pins (BioRobotics, Cambridge, UK). Relative humidity was controlled within the range 40-50% and temperature between 20-25°C. cDNA derived from 2µg of cRNA, essentially as described,7 was aminoallyl labeled8 with Cy5 (sample) or Cy3 (reference), hybridized overnight at 42ºC in a buffer containing 50% formamide, 5xSSC, 0.1% SDS, 0.25µg/µl human cot1 DNA and 0.125µg/µl poly dT and washed to a final stringency of 1x SSC at 42°C. After washing, slides were immediately scanned using an Axon GenePix 4000B scanner and quantified using Axon GenePix Pro software (Axon, Union city, CA). Raw data for all 40,386 elements across all 105 samples assayed here is deposited with\nFrom GPL962\nLast Updated: Sep 08 2006
#> 18: Patients and Sample Preparation. We analyzed NT samples from 38 patients undergoing surgery at the Cancer Institute Hospital, Tokyo, during May 1996 ? May 2001. All samples were collected with informed consent and ethical committee approval and were grossly dissected, snap-frozen in liquid nitrogen within 20 minutes of removal. Initial diagnosis of each sample from frozen section was later confirmed by detailed analysis of paraffin sections and immunohistochemistry. Following WHO guidelines,1 17 tumours were classified as SCLC including two combined SCLC with adenocarcinoma (SCLC-AD), 8 as LCNEC, including 2 combined LCNEC with AD (LCNEC-AD), 12 as TC and 1 as AC. The prevalence of LCNEC as a percentage all lung cancer resected at the Cancer Institute during the period was 2.7%. Since LCNEC is described as a variant of large cell carcinoma MAGE(LCC), we also analyzed thirteen LCC samples. Twelve well differentiated AD samples were included to aid interpretation of expression profiles for the SCLC-AD and LCNEC-AD samples, and to allow identification of markers that distinguish NT from non-small cell lung cancer. We included thirty normal lung samples from unrelated individuals. Finally 11 SCLC cell lines were incorporated into the analysis. Full clinical details of all tumour samples and cell lines are provided in supplementary table 1. Reference RNA, a mixture of lung cancer cell lines and normal lung, is exactly as described previously.5 Cell lines were obtained from the American Type Culture Collection. the Japanese Collection of Research Bioresources, or The RIKEN cell bank. cDNA microarray Each microarray contains 40,368 elements, of which 39,936 are derived from IMAGE cDNA clones purchased from Research Genetics (Huntsville, Alabama). This clone set was supplemented with 384 proprietary clones and 48 control elements. According to our latest estimate, the array represents 29,487 unique UNIGENE clusters accounting for 9,085 named genes, 15,276 ESTs and 5126 other un-named genes (for example, clones described as hypothetical proteins). Clones were purchased as sequence verified, but we estimate an error rate of at least 10%. Genes mentioned by name in this paper have been re-sequenced. cDNA PCR products were resuspended in 50% DMSO and printed at a pitch of 150 µm onto CMT-GAPS slides (Corning, Corning, NY) using a MicroGrid II spotting robot fitted with 10K pins (BioRobotics, Cambridge, UK). Relative humidity was controlled within the range 40-50% and temperature between 20-25°C. cDNA derived from 2µg of cRNA, essentially as described,7 was aminoallyl labeled8 with Cy5 (sample) or Cy3 (reference), hybridized overnight at 42ºC in a buffer containing 50% formamide, 5xSSC, 0.1% SDS, 0.25µg/µl human cot1 DNA and 0.125µg/µl poly dT and washed to a final stringency of 1x SSC at 42°C. After washing, slides were immediately scanned using an Axon GenePix 4000B scanner and quantified using Axon GenePix Pro software (Axon, Union city, CA). Raw data for all 40,386 elements across all 105 samples assayed here is deposited with\nFrom GPL962\nLast Updated: Sep 08 2006
#> 19: Patients and Sample Preparation. We analyzed NT samples from 38 patients undergoing surgery at the Cancer Institute Hospital, Tokyo, during May 1996 ? May 2001. All samples were collected with informed consent and ethical committee approval and were grossly dissected, snap-frozen in liquid nitrogen within 20 minutes of removal. Initial diagnosis of each sample from frozen section was later confirmed by detailed analysis of paraffin sections and immunohistochemistry. Following WHO guidelines,1 17 tumours were classified as SCLC including two combined SCLC with adenocarcinoma (SCLC-AD), 8 as LCNEC, including 2 combined LCNEC with AD (LCNEC-AD), 12 as TC and 1 as AC. The prevalence of LCNEC as a percentage all lung cancer resected at the Cancer Institute during the period was 2.7%. Since LCNEC is described as a variant of large cell carcinoma MAGE(LCC), we also analyzed thirteen LCC samples. Twelve well differentiated AD samples were included to aid interpretation of expression profiles for the SCLC-AD and LCNEC-AD samples, and to allow identification of markers that distinguish NT from non-small cell lung cancer. We included thirty normal lung samples from unrelated individuals. Finally 11 SCLC cell lines were incorporated into the analysis. Full clinical details of all tumour samples and cell lines are provided in supplementary table 1. Reference RNA, a mixture of lung cancer cell lines and normal lung, is exactly as described previously.5 Cell lines were obtained from the American Type Culture Collection. the Japanese Collection of Research Bioresources, or The RIKEN cell bank. cDNA microarray Each microarray contains 40,368 elements, of which 39,936 are derived from IMAGE cDNA clones purchased from Research Genetics (Huntsville, Alabama). This clone set was supplemented with 384 proprietary clones and 48 control elements. According to our latest estimate, the array represents 29,487 unique UNIGENE clusters accounting for 9,085 named genes, 15,276 ESTs and 5126 other un-named genes (for example, clones described as hypothetical proteins). Clones were purchased as sequence verified, but we estimate an error rate of at least 10%. Genes mentioned by name in this paper have been re-sequenced. cDNA PCR products were resuspended in 50% DMSO and printed at a pitch of 150 µm onto CMT-GAPS slides (Corning, Corning, NY) using a MicroGrid II spotting robot fitted with 10K pins (BioRobotics, Cambridge, UK). Relative humidity was controlled within the range 40-50% and temperature between 20-25°C. cDNA derived from 2µg of cRNA, essentially as described,7 was aminoallyl labeled8 with Cy5 (sample) or Cy3 (reference), hybridized overnight at 42ºC in a buffer containing 50% formamide, 5xSSC, 0.1% SDS, 0.25µg/µl human cot1 DNA and 0.125µg/µl poly dT and washed to a final stringency of 1x SSC at 42°C. After washing, slides were immediately scanned using an Axon GenePix 4000B scanner and quantified using Axon GenePix Pro software (Axon, Union city, CA). Raw data for all 40,386 elements across all 105 samples assayed here is deposited with\nFrom GPL962\nLast Updated: Sep 08 2006
#> 20: A microarray with 9216 spot features. Tip Configuration: Standard 16-tip Columns per Sector: 24 Rows per Sector: 24 Column Spacing: 200 Row Spacing: 200
#> platform.description
#> platform.troubled taxon.name taxon.scientific taxon.ID taxon.NCBI
#> <lgcl> <char> <char> <int> <int>
#> 1: FALSE human Homo sapiens 1 9606
#> 2: FALSE human Homo sapiens 1 9606
#> 3: FALSE human Homo sapiens 1 9606
#> 4: FALSE human Homo sapiens 1 9606
#> 5: FALSE human Homo sapiens 1 9606
#> 6: FALSE human Homo sapiens 1 9606
#> 7: FALSE human Homo sapiens 1 9606
#> 8: FALSE human Homo sapiens 1 9606
#> 9: FALSE human Homo sapiens 1 9606
#> 10: FALSE human Homo sapiens 1 9606
#> 11: FALSE human Homo sapiens 1 9606
#> 12: FALSE human Homo sapiens 1 9606
#> 13: FALSE human Homo sapiens 1 9606
#> 14: FALSE human Homo sapiens 1 9606
#> 15: FALSE mouse Mus musculus 2 10090
#> 16: FALSE human Homo sapiens 1 9606
#> 17: FALSE human Homo sapiens 1 9606
#> 18: FALSE human Homo sapiens 1 9606
#> 19: FALSE human Homo sapiens 1 9606
#> 20: FALSE human Homo sapiens 1 9606
#> platform.troubled taxon.name taxon.scientific taxon.ID taxon.NCBI
#> taxon.database.name taxon.database.ID
#> <char> <int>
#> 1: hg38 87
#> 2: hg38 87
#> 3: hg38 87
#> 4: hg38 87
#> 5: hg38 87
#> 6: hg38 87
#> 7: hg38 87
#> 8: hg38 87
#> 9: hg38 87
#> 10: hg38 87
#> 11: hg38 87
#> 12: hg38 87
#> 13: hg38 87
#> 14: hg38 87
#> 15: mm10 81
#> 16: hg38 87
#> 17: hg38 87
#> 18: hg38 87
#> 19: hg38 87
#> 20: hg38 87
#> taxon.database.name taxon.database.ID