Result

Search results for the GEO ID: GSE12948

(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

GSM324786

GPL1261

Control 2

Control

nonmalignant T cells

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324786
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 09 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324786/suppl/GSM324786.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324786/suppl/GSM324786.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324788

GPL1261

Abnormal non-malignant 2

Abnormal non-malignant

nonmalignant T cells

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324788
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324788/suppl/GSM324788.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324788/suppl/GSM324788.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324789

GPL1261

Abnormal non-malignant 3

Abnormal non-malignant

nonmalignant T cells

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324789
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324789/suppl/GSM324789.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324789/suppl/GSM324789.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324791

GPL1261

Control 1

Control

nonmalignant T cells

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324791
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 09 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324791/suppl/GSM324791.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324791/suppl/GSM324791.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324792

GPL1261

Abnormal non-malignant 1

Abnormal non-malignant

nonmalignant T cells

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324792
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324792/suppl/GSM324792.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324792/suppl/GSM324792.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324793

GPL1261

NIC Tumor 1

NIC Tumor

T-ALL

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324793
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324793/suppl/GSM324793.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324793/suppl/GSM324793.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324794

GPL1261

NIC Tumor 2

NIC Tumor

T-ALL

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324794
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324794/suppl/GSM324794.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324794/suppl/GSM324794.chp.gz
Sample_series_id	GSE12948
Sample_data_row_count	45101

GSM324796

GPL1261

NIC Tumor 3

NIC Tumor

T-ALL

standard processing performed by Microarray Core of DFCI

Sample_geo_accession	GSM324796
Sample_status	Public on Oct 27 2008
Sample_submission_date	Sep 26 2008
Sample_last_update_date	Oct 27 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
Sample_hyb_protocol	Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Sample_scan_protocol	Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
Sample_data_processing	Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
Sample_platform_id	GPL1261
Sample_contact_name	Alexei,,Protopopov
Sample_contact_department	IACS
Sample_contact_institute	UT MD Anderson Cancer Center
Sample_contact_address	1901 East Rd
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77054
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324796/suppl/GSM324796.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM324nnn/GSM324796/suppl/GSM324796.chp.gz
Sample_series_id	GSE12948
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