Result

Search results for the GEO ID: GSE23016

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Title

Source name

Description

Characteristics

GSM567848

GPL1261

AdV-NULL_mouse_1

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: NULL

Sample_geo_accession	GSM567848
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567848/suppl/GSM567848.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567849

GPL1261

AdV-NULL_mouse_2

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: NULL

Sample_geo_accession	GSM567849
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567849/suppl/GSM567849.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567850

GPL1261

AdV-NULL_mouse_3

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: NULL

Sample_geo_accession	GSM567850
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567850/suppl/GSM567850.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567851

GPL1261

AdV-IL4_mouse_1

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4

Sample_geo_accession	GSM567851
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567851/suppl/GSM567851.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567852

GPL1261

AdV-IL4_mouse_2

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4

Sample_geo_accession	GSM567852
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567852/suppl/GSM567852.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567853

GPL1261

AdV-IL4_mouse_3

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4

Sample_geo_accession	GSM567853
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567853/suppl/GSM567853.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567854

GPL1261

AdV-IL4d2_mouse_1

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4d2

Sample_geo_accession	GSM567854
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567854/suppl/GSM567854.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567855

GPL1261

AdV-IL4d2_mouse_2

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4d2

Sample_geo_accession	GSM567855
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567855/suppl/GSM567855.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

GSM567856

GPL1261

AdV-IL4d2_mouse_3

lung

strain: C57BL/6 gender: female age: 14 weeks tissue: lung

14 days after tntratracheal infection with replication-deficient adenovirus encoding: mouse Interleukin-4d2

Sample_geo_accession	GSM567856
Sample_status	Public on Mar 07 2011
Sample_submission_date	Jul 19 2010
Sample_last_update_date	Mar 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	After euthanasia, mouse lungs were collected, homogenized, and total RNA isolated using Trizol (Invitrogen).
Sample_growth_protocol_ch1	Sterile rodent microisolator caging, with filtered cage top.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Extraction of total RNA was performed using Trizol (Invitrogen) according to the manufacturer's instructions. Immediately prior to cDNA synthesis, the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) as per the manufacturers instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was processed and labeled according to standard RT-IVT methods. First and second strand cDNA were synthesized from 200 ng of total RNA using oligo-dT24-T7 (5’-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-3’) as primer and and cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription for 16hr at 37oC, using the 3’ IVT Express cDNA/cRNA Synthesis and Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.
Sample_hyb_protocol	Labeled cRNA (15.0 ug) was fragmented by ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix Mouse Genome 430 2.0 short oligomer arrays.
Sample_scan_protocol	Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner and AGCC software (Affymetrix)
Sample_data_processing = The scanned images were analyzed using Expression Console v2.0 software (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined after background correction and signal summarization by MAS 5.0 statistical algorithms resident in GCOS and standardization of each array by global scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (TGT) of 250. Expression data were analyzed following background correction, probe set signal summarization and normalization by MAS5.0 with global scaling (TGT	250). (Lockhart et al, 1996, Nat. Biotechnol. 14:1675-1680; Liu et al, 2002, Bioinformatics 18:1593-9; Hubbell et al, 2002, Bioinformatics 18(12):1585-92, Irizarry et al, 2006, Bioinformatics 22(7):789-94, and references therein). Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pairwise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed MAS5.0 signal values; probe set clustering was performed by the UPGMA method (Unweighted Pair Group Method using Arithmetic averages) using Pearson correlation as the similarity metric. Gene annotation, gene ontology information and biochemical pathway information were obtained from the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov), NetAffx (ww.affymetrix.com), the Gene Ontology Consortium (http://amigo.geneontology.org), the Kyoto Encyclopedia of Genes and Genomes (www.genome.jp/kegg), and WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt). Significant enrichment of specific GO categories or KEGG pathways in each comparison is estimated by hypergeometric tests.
Sample_platform_id	GPL1261
Sample_contact_name	Sergei,,Atamas
Sample_contact_email	satamas@umaryland.edu
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	10 S. Pine St., MSTF 834
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM567nnn/GSM567856/suppl/GSM567856.CEL.gz
Sample_series_id	GSE23016
Sample_data_row_count	45101

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