Result

Search results for the GEO ID: GSE46091

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Title

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Description

Characteristics

GSM1123174

GPL1261

WT DN3 cells, DMSO treated, rep1

genotype/variation: WT cell type: DN3 cells treatment: DMSO

Sample_geo_accession	GSM1123174
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123174/suppl/GSM1123174_WT_D1.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123175

GPL1261

WT DN3 cells, DMSO treated, rep2

genotype/variation: WT cell type: DN3 cells treatment: DMSO

Sample_geo_accession	GSM1123175
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123175/suppl/GSM1123175_WT_D2.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123176

GPL1261

WT DN3 cells, GSI treated, rep1

genotype/variation: WT cell type: DN3 cells treatment: gamma secretase inhibitor MRK-003

Sample_geo_accession	GSM1123176
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123176/suppl/GSM1123176_WT_G1.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123177

GPL1261

WT DN3 cells, GSI treated, rep2

genotype/variation: WT cell type: DN3 cells treatment: gamma secretase inhibitor MRK-003

Sample_geo_accession	GSM1123177
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123177/suppl/GSM1123177_WT_G2.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123178

GPL1261

IkL/L DN3 cells, DMSO treated, rep1

genotype/variation: IkL/L cell type: DN3 cells treatment: DMSO

Sample_geo_accession	GSM1123178
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123178/suppl/GSM1123178_IK_D1.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123179

GPL1261

IkL/L DN3 cells, DMSO treated, rep2

genotype/variation: IkL/L cell type: DN3 cells treatment: DMSO

Sample_geo_accession	GSM1123179
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123179/suppl/GSM1123179_IK_D2.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123180

GPL1261

IkL/L DN3 cells, GSI treated, rep1

genotype/variation: IkL/L cell type: DN3 cells treatment: gamma secretase inhibitor MRK-003

Sample_geo_accession	GSM1123180
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123180/suppl/GSM1123180_IK_G1.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

GSM1123181

GPL1261

IkL/L DN3 cells, GSI treated, rep2

genotype/variation: IkL/L cell type: DN3 cells treatment: gamma secretase inhibitor MRK-003

Sample_geo_accession	GSM1123181
Sample_status	Public on Apr 17 2013
Sample_submission_date	Apr 16 2013
Sample_last_update_date	Apr 17 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.
Sample_growth_protocol_ch1	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.
Sample_hyb_protocol	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).
Sample_scan_protocol	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
Sample_data_processing	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.
Sample_platform_id	GPL1261
Sample_contact_name	Susan,,Chan
Sample_contact_email	scpk@igbmc.fr
Sample_contact_phone	33 3 88 65 34 72
Sample_contact_fax	33 3 88 65 32 01
Sample_contact_institute	IGBMC
Sample_contact_address	1, rue Laurent Fries
Sample_contact_city	Illkirch
Sample_contact_zip/postal_code	67404
Sample_contact_country	France
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1123nnn/GSM1123181/suppl/GSM1123181_IK_G2.CEL.gz
Sample_series_id	GSE46091
Sample_data_row_count	45101

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