Result

Search results for the GEO ID: GSE19091

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM472979

GPL1261

393P, control A

393P lung cancer cell line, control

cell line: 393P cell type: lung tumor vector: control

393P cells with control vector (393P-scr), sample 1 of 3. H0022313

Sample_geo_accession	GSM472979
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472979/suppl/GSM472979.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

GSM472980

GPL1261

393P, control B

393P lung cancer cell line, control

cell line: 393P cell type: lung tumor vector: control

393P cells with control vector (393P-scr), sample 2 of 3. H0022314

Sample_geo_accession	GSM472980
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472980/suppl/GSM472980.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

GSM472981

GPL1261

393P, control C

393P lung cancer cell line, control

cell line: 393P cell type: lung tumor vector: control

393P cells with control vector (393P-scr), sample 3 of 3. H0022315

Sample_geo_accession	GSM472981
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472981/suppl/GSM472981.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

GSM472982

GPL1261

393P, MKK4shRNA A

393P lung cancer cell line, MKK4 knockdown

cell line: 393P cell type: lung tumor vector: MKK4 shRNA

393P cells with MKK4 knockdown (393P-shZ), sample 1 of 3. H0022316

Sample_geo_accession	GSM472982
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472982/suppl/GSM472982.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

GSM472983

GPL1261

393P, MKK4shRNA B

393P lung cancer cell line, MKK4 knockdown

cell line: 393P cell type: lung tumor vector: MKK4 shRNA

393P cells with MKK4 knockdown (393P-shZ), sample 2 of 3. H0022317

Sample_geo_accession	GSM472983
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472983/suppl/GSM472983.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

GSM472984

GPL1261

393P, MKK4shRNA C

393P lung cancer cell line, MKK4 knockdown

cell line: 393P cell type: lung tumor vector: MKK4 shRNA

393P cells with MKK4 knockdown (393P-shZ), sample 3 of 3. H0022318

Sample_geo_accession	GSM472984
Sample_status	Public on Oct 01 2011
Sample_submission_date	Nov 18 2009
Sample_last_update_date	Oct 01 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Vectors expressing mouse MKK4 shRNA were purchased from OriGene. Cells were transfected using Lipofectamine-PlusTM (Invitrogen).
Sample_growth_protocol_ch1	Cell lines from p53R172H∆g/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy. The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (393P).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner.
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM472nnn/GSM472984/suppl/GSM472984.CEL.gz
Sample_series_id	GSE19091
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes