Result

Search results for the GEO ID: GSE29110

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM720963

GPL1355

lung_control_1

lung, from control

tissue: Lung strain: Lewis treatment: control

Sample_geo_accession	GSM720963
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720963/suppl/GSM720963.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

GSM720964

GPL1355

lung_control_2

lung, from control

tissue: Lung strain: Lewis treatment: control

Sample_geo_accession	GSM720964
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720964/suppl/GSM720964.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

GSM720965

GPL1355

lung_control_3

lung, from control

tissue: Lung strain: Lewis treatment: control

Sample_geo_accession	GSM720965
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720965/suppl/GSM720965.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

GSM720966

GPL1355

lung_silica_1

lung, chronically exposed to silica

tissue: Lung strain: Lewis treatment: exposed to silica

Sample_geo_accession	GSM720966
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720966/suppl/GSM720966.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

GSM720967

GPL1355

lung_silica_2

lung, chronically exposed to silica

tissue: Lung strain: Lewis treatment: exposed to silica

Sample_geo_accession	GSM720967
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720967/suppl/GSM720967.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

GSM720968

GPL1355

lung_silica_3

lung, chronically exposed to silica

tissue: Lung strain: Lewis treatment: exposed to silica

Sample_geo_accession	GSM720968
Sample_status	Public on Jan 01 2012
Sample_submission_date	May 06 2011
Sample_last_update_date	Jan 01 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	polyA RNA
Sample_extract_protocol_ch1	Lung tissues were homogenized in the presence of TRI reagent (MRC Molecular Research Center, Cincinnati, OH). Total RNA was isolated using the 1-bromo-3-chloropropane (BCP) phase separation reagent (MRC Molecular Research Center). RNA was precipitated by 2-propanol and washed with 75% ethanol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA was synthesized by in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix).
Sample_hyb_protocol	Biotin-labeled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix), and 20 mg of the labeled cRNA was fragmented. The cRNA and fragmented cRNA quality was assessed by the Agilent 2100 Bioanalyzer (Agilent; Foster City, CA) and the RNA 6000 Nano LabChip kit (Agilent). The labeled fragmented cRNA was hybridized to Affymetrix GeneChip Rat 230 2.0 arrays for 16 h at 45oC following the Affymetrix protocol specific to this array type. Washing and staining were performed on the Affymetrix fluidics (450) station according to the antibody amplification protocol (Fluidics script: EukGE-WS2v5).
Sample_scan_protocol	The Gene Chips were scanned using the GeneChip Scanner 3000 (Affymetrix).
Sample_data_processing	The analysis was performed with GeneSpring software package (Agilent Technologies, Santa Clara, CA). All samples were subject to per-chip normalization. Data were filtered twice, a fold change filter (2 fold up or down), and the Statistical Analysis of Microarray software (http://www-stat.stanford.edu/~tibs/SAM/), to find all genes with a < 10% false positive q-score.
Sample_platform_id	GPL1355
Sample_contact_name	Raymond,J,Langley
Sample_contact_email	rlangley@lrri.org
Sample_contact_phone	505-348-9614
Sample_contact_laboratory	324
Sample_contact_department	immunology
Sample_contact_institute	LRRI
Sample_contact_address	2425 Ridgecrest Dr
Sample_contact_city	Albuquerque
Sample_contact_state	New Mexico
Sample_contact_zip/postal_code	87108
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM720nnn/GSM720968/suppl/GSM720968.CEL.gz
Sample_series_id	GSE29110
Sample_data_row_count	31099

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